diff --git a/changelog.md b/changelog.md index 23453d7da7..00be00cb66 100644 --- a/changelog.md +++ b/changelog.md @@ -24,7 +24,7 @@ A **changelog** is a structured record of changes made to the codebase over time v1.0.0 ### Next Version Updates - +- [2865](https://github.com/RuminantFarmSystems/RuFaS/pull/2865) - [minor change] [NoInputChange] [NoOutputChange] Update to tables and formatting in scientific documentation. - [2727](https://github.com/RuminantFarmSystems/RuFaS/pull/2727) - [minor change] [NoInputChange] [NoOutputChange] Update the TaskType in Wiki, and fix the broken Sphinx action. - [2728](https://github.com/RuminantFarmSystems/MASM/pull/2728) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Enforces the required file blobs. - [2743](https://github.com/RuminantFarmSystems/RuFaS/pull/2743) - [minor change] [NoInputChange] [NoOutputChange] Fix broken IM unit test. diff --git a/docs/scientific/animal.aux b/docs/scientific/animal.aux index 1f78ca70ea..88eb8b3256 100644 --- a/docs/scientific/animal.aux +++ b/docs/scientific/animal.aux @@ -1,25 +1,22 @@ \relax \providecommand\hyper@newdestlabel[2]{} -\@writefile{toc}{\contentsline {section}{\numberline {I.}Preface: A Day in the Life on a RuFaS Farm}{8}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {paragraph}{Feeding the Animals}{8}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {paragraph}{Taking Care of the Animals}{8}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {paragraph}{Dealing with the Manure}{9}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {paragraph}{Managing the Fields}{9}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {paragraph}{Storing the Feeds}{9}{section.1}\protected@file@percent } -\@writefile{toc}{\contentsline {section}{\numberline {II.}Module Introduction}{9}{section.2}\protected@file@percent } -\newlabel{refsection:1}{{II.}{9}{Module Introduction}{section.2}{}} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.}Animal Life Cycle}{10}{subsection.2.1}\protected@file@percent } +\@writefile{toc}{\contentsline {part}{II\hspace {1em}Animal Module}{6}{part.2}\protected@file@percent } +\@writefile{toc}{\etoc@startlocaltoc{2}} +\@writefile{toc}{\etoc@startlocaltoc{3}} +\@writefile{toc}{\etoc@startlocaltoc{4}} +\@writefile{toc}{\contentsline {section}{\numberline {1}Module Introduction}{10}{section.1}\protected@file@percent } +\newlabel{refsection:1}{{1}{10}{Module Introduction}{section.1}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.a}Animal Life Cycle}{10}{subsection.1.1}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {2}Herd-level Processes and Management}{11}{section.2}\protected@file@percent } +\@writefile{toc}{\contentsline {subsection}{\numberline {2.a}Herd Initialization}{11}{subsection.2.1}\protected@file@percent } +\newlabel{herdinit}{{2.a}{11}{Herd Initialization}{subsection.2.1}{}} +\@writefile{toc}{\contentsline {paragraph}{Introduction}{11}{subsection.2.1}\protected@file@percent } \gdef \LT@i {\LT@entry {5}{148.26378pt}\LT@entry - {5}{154.26378pt}\LT@entry + {1}{163.35333pt}\LT@entry {5}{148.26378pt}} -\@writefile{toc}{\contentsline {section}{\numberline {III.}Herd-level Processes and Management}{11}{section.3}\protected@file@percent } -\newlabel{sec:AnManage}{{III.}{11}{Herd-level Processes and Management}{section.3}{}} -\@writefile{toc}{\contentsline {subsection}{\numberline {A.}Herd Initialization}{11}{subsection.3.1}\protected@file@percent } -\newlabel{sec:animalINPUTS}{{A.}{11}{Herd Initialization}{subsection.3.1}{}} -\newlabel{herdinit}{{A.}{11}{Herd Initialization}{subsection.3.1}{}} -\@writefile{toc}{\contentsline {paragraph}{Introduction}{11}{subsection.3.1}\protected@file@percent } -\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{11}{table.1}\protected@file@percent } +\@writefile{toc}{\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{12}{table.1}\protected@file@percent } +\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{12}{table.1}\protected@file@percent } \gdef \LT@ii {\LT@entry {5}{148.26378pt}\LT@entry {5}{211.16928pt}\LT@entry @@ -32,62 +29,62 @@ {2}{68.9055pt}\LT@entry {2}{68.9055pt}\LT@entry {2}{62.9055pt}} -\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). 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\makebox[\textwidth]{% - \includegraphics[height=40pt]{resources/rufas.png}\hfill - \textbf{\today}% - } - }\\[-25pt] - \centering\textbf{Scientific Documentation of RuFaS Model} \\ - \rule{\textwidth}{1pt} -} - - -% Footer setup with a divider line and two lines of text on left and right -\renewcommand{\footrulewidth}{0.4pt} -\fancyfoot[L]{% - \begin{tabular}[t]{@{}l@{}} - Ruminant Farm System\\ - Sci Doc v.1 - \end{tabular}% -} -\fancyfoot[C]{\thepage} % Center: page number -\fancyfoot[R]{% - \begin{tabular}[t]{@{}r@{}} - \nouppercase{\leftmark}\\ % This pulls in the current section title - \end{tabular}% -} -% Landscape pages should be blank (no headers/footers) -\fancypagestyle{landscapeplain}{ - \fancyhf{} % clear all - \renewcommand{\headrulewidth}{0pt} - \renewcommand{\footrulewidth}{0pt} -} - - -% Bibliography setup -\usepackage[ - backend=biber, - style=authoryear, % You can change this to numeric, apa, etc. - natbib=true % Enables \citep, \citet if desired -]{biblatex} - 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-\titlespacing{\subsection}{0pt}{8pt plus 1pt minus 1pt}{4pt} -\titlespacing{\subsubsection}{0pt}{6pt plus 1pt minus 1pt}{3pt} - -% Optional: Keep your TOC control if needed -\usepackage{etoc} - -% Optional: If using headers/footers -\renewcommand{\sectionmark}[1]{\markboth{#1}{}} - - -% Remove default date from title -\date{} % Prevents date from appearing in \maketitle - - -% Define title -\title{\textbf{}} -\author{ } -\setlength{\topskip}{10pt} % Ensures LaTeX reserves room above the first line -%\usepackage{showframe} - -\begin{document} - -% Custom Title Page -\begin{titlepage} - \thispagestyle{empty} - \centering - \vspace*{2cm} - - {\Huge\bfseries Ruminant Farm System Model\par} - \vspace{1cm} - - {\Large Animal Module\par} - \vspace{1cm} - - {\large \today\par} - \vspace{1.5cm} % Add space before the image - - \includegraphics[width=0.25\textwidth]{resources/animal1.png} % Adjust size and filename - - \vfill - - {\small v.1; Updated 2025\par} - \vspace*{1cm} -\end{titlepage} - - -\newpage - - -% Continue with front matter (e.g., table of contents) -\thispagestyle{fancy} % Ensure the header/footer appears on the first page - +\part{Animal Module} % Global Table of Contents \thispagestyle{fancy} -\tableofcontents -\newpage - -\listoffigures +% Local TOC that includes only what’s inside THIS section +\etocsettocstyle{\subsection*{Contents}}{} % heading for the local toc +\etocsetnexttocdepth{subsection} % or subsubsection +\localtableofcontents \newpage -\listoftables +\section*{List of Figures} +\locallistoffigures \newpage -% --- Global Structure --- -\section{Preface: A Day in the Life on a RuFaS Farm} - -This document provides a high-level overview of the daily operations of a ruminant farm, as modeled by RuFaS. The overview will be through the eyes of Dr. Rue Fas. One day, Dr. Rue woke up and decided the life of a computer scientist wasn’t for her. So she bought a dairy farm, and this is how she operates it every day. - -\paragraph{Feeding the Animals} -Second thing in the morning, after coffee, Dr. Rue checks the calendar to see if it’s time to formulate a new ration for her animals. -\vspace{0.2cm} - -If a new ration needs to be formulated, Dr. Rue heads over to the barn where she keeps all her forages and feed. While there, she checks how well all the forages are holding up. After considering the feeds available, the quality of each one, and how much each one costs, she decides on how productive she wants her animals to be. It is a difficult balancing act, but eventually a ration recipe is found that will keep the animals happy while keeping costs low and sustainability high until the calendar says the ration recipe needs to be reformulated. -\vspace{0.2cm} - -When Dr. Rue doesn’t need to formulate a new ration, she takes the last ration recipe she made and grabs all the feed and forage the animals need for the day out of the feed barn. If there isn’t enough for the animals, then a new ration is formulated using the steps above. - -\paragraph{Taking Care of the Animals} -After making sure all the animals’ feed is taken care of, Dr. Rue moves on to taking care of all the other animal tasks. This includes milking the animals, making sure they’re healthy, getting them pregnant, and numerous other tasks. -\vspace{0.2cm} - -As dawn breaks on the RuFaS farm, the animals awaken after a restful night. Joe, the farm master, prepares a large whiteboard to track HerdReproductionStatistics, ensuring he has all the data he needs for the day’s activities. - -\textit{Daily Routine} - After leaving their pens, each animal lines up in front of the barn. Julie, the diligent farm veterinarian, examines them one by one. This daily check includes updates on the following areas: -\begin{itemize} - \item Nutrients: Each animal begins its day with a quick phosphorus requirement assessment. Julie records these details and updates the animal’s phosphorus-related metrics. - \item Digestive System: With nutrient information in hand, Julie shifts focus to each animal’s digestive system, estimating manure output and enteric methane production for that day. - - \item Milk Production: All milking cows are assessed to gauge daily milk yield and milk component content (fat and protein). Any necessary adjustments are noted. - - \item Animal Growth: Around midday, Julie returns to each animal to evaluate daily weight changes. She updates each animal’s body weight accordingly. - - \item Reproduction: HeiferII and Cow stage animals undergo a reproduction check. Julie closely monitors their reproductive progress and updates the HerdReproductionStatistics details on Joe’s whiteboard. - - \item Life Stage Evaluation: Once the daily routines are complete, Julie determines if any animal is ready to progress to the next life stage. Graduating animals are marked as “graduated” to be moved to their new pens. Animals that must leave the herd—due to health, productivity, or other issues—are labeled as “sold” or “dead” to be removed from the farm population. - - \item Herd Size Maintenance: After every animal has been evaluated, Joe counts the herd to ensure it remains at a healthy size. If it is too large, he arranges the sale of some animals. If the herd is too small, he may opt to purchase additional heiferIIIs to keep numbers at the ideal level. - - \item Herd Structure Management: Joe also manages pen assignments. Newly graduated or newborn animals are guided to suitable pens, while animals marked for removal (sold or deceased) are taken out of the herd and removed from the farm records. -\end{itemize} - - -\textit{Output Reporting} -At day’s end, Joe and Julie review the updated HerdReproductionStatistics on the whiteboard. Joe then compiles a concise report summarizing the day’s herd stats. He forwards this information to the OutputManager before wrapping up another successful day on the RuFaS farm. -\vspace{0.5cm} - -\paragraph{Dealing with the Manure} -Once all the animal chores are finished, Dr. Rue moves on to handling the manure. There are a lot of different ways that manure is collected from the animals: it is flushed out of the milking parlor with water, some of the pens need to have it shoveled out along with the bedding in the pen, and some pens have grates that allow the manure to go straight into a pit beneath the barn. -\vspace{0.2cm} - -There are a lot of different places where manure is processed and stored on the farm. Dr. Rue goes from place to place on the farm, moving the manure from one place to the next. The manure chores are finished after moving all of the manure into her lagoons, compost piles, and other storages. As this final manure chore is completed, she writes down all the information about how much manure is in all these storages, and some information about what that manure is made of. How much water, nitrogen, phosphorus, other solids, etc. are in each storage. - -\paragraph{Managing the Fields} -Now that Dr. Rue is done making sure all the manure has been handled and stored properly, she can take care of all the field tasks. She has a lot of fields on her farm, each with its own unique schedule. Her field management routine starts with checking each field’s schedule to see if any of them are due to have manure applied, and if so, how much they should have applied. After noting all the manure that is supposed to go onto her fields, these amounts are checked against the amounts of manure that are in her manure storage. Dr. Rue then applies manure to each field on the schedule that day, trying to match the amount applied to the amount on the schedule as best she can. -\vspace{0.2cm} - -After making sure every manure item on each farm’s schedule has been taken care of for the day, the schedule for each field is rechecked, one field at a time. In each schedule she checks to see if that field needs to be tilled, if any chemical fertilizer needs to be applied, and if any crops need to be planted or harvested. After all these activities are taken care of, Mother Nature goes to work. The sun shines and rain falls, providing the field with water and energy that grows crops and soaks the soil. After taking care of each field one by one, Dr. Rue drives back to the main farm with all of the crops that she harvested on that day. - -\paragraph{Storing the Feeds} -Now that she is back at the barns, all the crops that were just harvested can be stored. Fortunately she is very organized, so all her harvested crops are separate from one another and each has a label, indicating where it will be stored inside the feed barn. As each feed is stored, it is labeled with the current date. Dr. Rue is exhausted from another long day. She goes back to the farmhouse and rests up, preparing to do the whole thing over again tomorrow. Her daily routine might seem repetitive, but each day is a crucial part of the larger, continuous process that keeps her farm running efficiently and sustainably. - - - - +\section*{List of Tables} +\locallistoftables +\newpage \section{Module Introduction} \begin{refsection} + \par\noindent\justifying The Animal Module simulates individual animals on a daily basis throughout each stage of life from birth until removal from the herd. In addition to the dynamic Monte-Carlo models that determine the occurrence of events throughout each animal’s life, the Animal Module uses process-based, dynamic models to simulate the following processes: \begin{figure}[H] @@ -271,9 +41,11 @@ \section{Module Introduction} \end{itemize} \end{minipage} \end{figure} +\par\noindent\justifying + Animals in the RuFaS model are divided into 5 life stages and a culling stage that were established based on the different management and physiological processes that need to be simulated for each class. The 5 classes and culling stage are described in more detail later in this document, but include: calves, heifers I, heifers II, heifers III, cow, and culled. -The attributes that define the animal characteristics and management are provided by the user and are comprehensively described in \hyperref[sec:animalINPUTS]{inputs section} of this module. When a simulation begins, the herd is populated by a semi-random draw of animals from a large, existing set of animal objects. This process and the process for regenerating the population of animals used to initialize the herd are described in detail in the \hyperref[herdinit]{Herd Initialization Section}. The initially selected animal objects are then grouped into pens based on their life stage and the user-provided pen information. Once the herd has been set up, a regular progression of functions is called each day to simulate and report outputs of the processes required to manage the herd and the processes that define each animal’s development and production. These daily updates are grouped into two classes in the RuFaS model: herd level daily routines (HerdManager) and animal level daily routines (AnimalManager). At the start of each day, the Herd-level daily update cycles through all the animals to call their daily update functions. Then based on the changes for each animal that resulted from the animal level daily updates, the HerdManager changes the animal life-stages, moves them to new pens, and removes them from the herd. If the herd size has decreased too much, the HerdManager will purchase new Heifer III animals to maintain the adult herd size. The HerdManager then checks if it is time to formulate a new diet (at a user-specified interval), summarizes and reports the herd statistics, and gathers and reports all of the manure excreted by the animals to pass to the Manure Module. +The attributes that define the animal characteristics and management are provided by the user and are comprehensively described in the inputs section of this module. When a simulation begins, the herd is populated by a semi-random draw of animals from a large, existing set of animal objects. This process and the process for regenerating the population of animals used to initialize the herd are described in detail in the \hyperref{herdinit}{Herd Initialization Section}. The initially selected animal objects are then grouped into pens based on their life stage and the user-provided pen information. Once the herd has been set up, a regular progression of functions is called each day to simulate and report outputs of the processes required to manage the herd and the processes that define each animal’s development and production. These daily updates are grouped into two classes in the RuFaS model: herd level daily routines (HerdManager) and animal level daily routines (AnimalManager). At the start of each day, the Herd-level daily update cycles through all the animals to call their daily update functions. Then based on the changes for each animal that resulted from the animal level daily updates, the HerdManager changes the animal life-stages, moves them to new pens, and removes them from the herd. If the herd size has decreased too much, the HerdManager will purchase new Heifer III animals to maintain the adult herd size. The HerdManager then checks if it is time to formulate a new diet (at a user-specified interval), summarizes and reports the herd statistics, and gathers and reports all of the manure excreted by the animals to pass to the Manure Module. Daily outputs from the Animal module are provided at a variety of scales and time steps that range from reports at the individual animal level (e.g. animal event histories), animal class level (e.g. average dry-matter intake for Heifer II’s), at the pen level (e.g. average net energy requirement or intake for Pen 3), and at the herd level (i.e. number of animals sold each day). A complete list of potential outputs from the Animal Module is provided in this document. \vspace{1cm} @@ -304,9 +76,11 @@ \subsection{Animal Life Cycle} -\section{Herd-level Processes and Management}\label{sec:AnManage} - -\subsection{Herd Initialization} \label{sec:animalINPUTS}\label{herdinit} +\section{Herd-level Processes and Management} +\vspace{0.5cm} + +\subsection{Herd Initialization} \label{herdinit} +\vspace{0.5cm} \begin{tcolorbox}[colback=white, colframe=black, title=Important Note] \textit{In RuFaS code, the term “herd initialization” is used to refer to both the process of generating an animal population file and of selecting from that population to create a specific herd at the start of a simulation. In this doc, those two processes will be differentiated by calling them “Generation” and “Selection”, respectively. } @@ -518,7 +292,7 @@ \subsection{Herd Initialization} \label{sec:animalINPUTS}\label{herdinit} -\subsection{Pens and Animal Grouping} \label{animgen} +\subsection{Pens and Animal Grouping} \paragraph{Introduction} All animals in RuFaS are assigned to a pen which is used to summarize nutrient requirements for diet formulation and feeding, aggregate enteric methane and manure excretions for reporting and passage to the Manure Module. Each pen tracks and updates daily a list of animals in the pen, the stocking density, the average nutrient requirement of the animals in the pen, the ration being fed to that pen, the manure excreted, and the methane emitted. In addition, constant attributes of each pen include the type of pen it is (freestall, tiestall, open lot, compost bedded pack barn), the type of animals that can be in that pen, the number stalls, the manure management practices associated with that pen, and the distance to the milking parlor for lactating cows. Each day after the HerdManager has updated the status of each animal and determined which animals need to be bought or sold, the animals are added and removed from pens as needed. @@ -678,7 +452,7 @@ \subsection{Ration Formulation} \subsubsection{Energy and Nutrition Requirements} -\paragraph{NRC: Calculating Nutrient Requirements of Dairy Cattle} \label{sec:enreq} +\paragraph{NRC: Calculating Nutrient Requirements of Dairy Cattle} Below are the calculations utilized based on the energy and nutrient requirements of dairy cattle as reported by the NRC and more recently the NASEM \parencite{nrc2001, nrc2021}. \vspace{0.2cm} @@ -696,9 +470,9 @@ \subsubsection{Energy and Nutrition Requirements} Where appropriate, requirement calculations are differentiated by animal age and reproductive status. \vspace{0.5cm} -\subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} +\subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} - \textbf{ Energy Requirements} For details about the variables included in each calculation, please refer to the \hyperref[energykey]{energy requirements key}. + \textbf{ Energy Requirements} For details about the variables included in each calculation, please refer to the energy requirements key. \vspace{0.2cm} \begin{itemize} @@ -985,7 +759,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \end{itemize} - \textbf{ Protein Requirements} Reporting of protein requirements is divided into 4 components: maintenance, growth, pregnancy, and lactation (all in metabolizable protein). For details about the variables included in each calculation, please refer to the \hyperref[proteinkey]{protein requirements key}. + \textbf{ Protein Requirements} Reporting of protein requirements is divided into 4 components: maintenance, growth, pregnancy, and lactation (all in metabolizable protein). For details about the variables included in each calculation, please refer to the protein requirements key. \vspace{0.2cm} \begin{itemize} @@ -1110,7 +884,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{3.5cm} L{2.5cm} @{}} -\caption{Key variables used in protein requirement calculations.} \label{proteinkey} \\ +\caption{Key variables used in protein requirement calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -1139,7 +913,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \textbf{ Mineral Requirements} \begin{tcolorbox}[colback=white, colframe=black, title=Important Note] - Only calcium (Ca) and phosphorus (P) requirements are considered currently. For details about the variables included in each calculation, please refer to the \hyperref[minkey]{mineral requirements key}. + Only calcium (Ca) and phosphorus (P) requirements are considered currently. For details about the variables included in each calculation, please refer to the mineral requirements key. \end{tcolorbox} \begin{itemize} @@ -1291,7 +1065,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{3.5cm} L{2.5cm} @{}} -\caption{Key variables used in mineral requirement calculations.} \label{minkey} \\ +\caption{Key variables used in mineral requirement calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -1394,7 +1168,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{2.5cm} L{3.5cm} L{4.5cm} @{}} -\caption{Key variables used in DMI requirement calculations.} \label{dmikey} \\ +\caption{Key variables used in DMI requirement calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -1425,9 +1199,10 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} -\paragraph{NASEM: Calculating Nutrient Requirements of Dairy Cattle: Eighth Revised Edition} \label{sec:NASEM} +\paragraph{NASEM: Calculating Nutrient Requirements of Dairy Cattle: Eighth Revised Edition} - \textbf{ Energy Requirements} The maintenance requirement is calculated based on metabolic body weight (MBW, body weight\(^{0.75}\)) adjusted for the tissues associated with pregnancy. For details about the variables included in each calculation, please refer to the \hyperref[nasemenergykey]{energy requirements key}. + \textbf{ Energy Requirements} + The maintenance requirement is calculated based on metabolic body weight (MBW, body weight\(^{0.75}\)) adjusted for the tissues associated with pregnancy. For details about the variables included in each calculation, please refer to the energy requirements key. \vspace{0.2cm} \begin{itemize} @@ -1665,7 +1440,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} Each physiological function is quantified in terms of TP (true protein), instead of CP (crude protein). \vspace{0.2cm} - To convert both net protein and net amino acid values to a metabolizable basis, net values have to be divided into the calculated efficiencies for each physiological function. Efficiencies can be either fixed or combined for lactating cows. For simplicity, requirements were included on a fixed basis. For details about the variables included in each calculation, please refer to the \hyperref[nasemproteinkey]{protein requirements key}. + To convert both net protein and net amino acid values to a metabolizable basis, net values have to be divided into the calculated efficiencies for each physiological function. Efficiencies can be either fixed or combined for lactating cows. For simplicity, requirements were included on a fixed basis. For details about the variables included in each calculation, please refer to the protein requirements key. \vspace{0.5cm} \begin{itemize} @@ -1848,7 +1623,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in protein requirement calculations.} \label{nasemproteinkey} \\ +\caption{Key variables used in protein requirement calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -1892,7 +1667,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \vspace{0.5cm} -\textbf{ Mineral Requirements} Only calcium and phosphorus requirements are included in the code at present. For details about the variables included in each calculation, please refer to the \hyperref[nasemminkey]{mineral requirements key}. +\textbf{ Mineral Requirements} Only calcium and phosphorus requirements are included in the code at present. For details about the variables included in each calculation, please refer to the mineral requirements key. \vspace{0.5cm} \begin{itemize} @@ -2028,7 +1803,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in mineral requirement calculations.} \label{nasemminkey} \\ +\caption{Key variables used in mineral requirement calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -2068,7 +1843,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \end{longtable} \vspace{0.5cm} -\textbf{ Dry Matter Intake Estimation} Dry matter intake estimation is different for lactating cows and dry cows. The sum of the dry matter intake of each feed is assumed to be less than the dry matter intake estimation For details about the variables included in each calculation, please refer to the \hyperref[nasemdmikey]{DMI estimation key}. +\textbf{ Dry Matter Intake Estimation} Dry matter intake estimation is different for lactating cows and dry cows. The sum of the dry matter intake of each feed is assumed to be less than the dry matter intake estimation For details about the variables included in each calculation, please refer to the DMI estimation key. \vspace{0.5cm} \begin{center} @@ -2102,7 +1877,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in DMI estimation calculations.} \label{nasemdmikey} \\ +\caption{Key variables used in DMI estimation calculations.} \\ \toprule \textbf{Variable} & \textbf{Description} & \textbf{Units} \\ \midrule @@ -2131,8 +1906,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \end{longtable} \vspace{0.5cm} -\paragraph{NASEM: Calculating Amino Acid Requirements} \label{sec:NASEMAA} - +\paragraph{NASEM: Calculating Amino Acid Requirements} The methods for estimating the amino acids requirements for lactating cows based on the \textcite{nrc2021}, into RuFaS are described below. \begin{itemize} \item Amino acids are divided into essential (EAA) and non-essential (NEAA). @@ -2143,7 +1917,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{3.5cm} @{}} -\caption{Essential and non-essential amino acids} \label{nasemdmikey} \\ +\caption{Essential and non-essential amino acids} \\ \toprule \textbf{Essential (EAA)} & \textbf{Non-essential (NEAA)} \\ \midrule @@ -2269,7 +2043,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{5cm} L{5.5cm} L{2.5cm} @{}} -\caption{Key variables used in calculation of AA.} \label{nasemminkey} \\ +\caption{Key variables used in calculation of AA.} \\ \toprule \multicolumn{1}{c}{\textbf{Variable}} & @@ -2339,7 +2113,7 @@ \subsubsection{Nutrient Requirements of Dairy Cattle (NRC)} \label{sec:NRC} -\subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} +\subsubsection{Energy and Nutrition Supply } \vspace{0.25cm} \paragraph{Nutrient Supply} @@ -2484,7 +2258,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in calculation of net energy in NRC 2001.} \label{nasemminkey} \\ +\caption{Key variables used in calculation of net energy in NRC 2001.} \\ \toprule \multicolumn{1}{c}{\textbf{Variable}} & \multicolumn{1}{c}{\textbf{Description}} & @@ -2676,7 +2450,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in calculation of net energy supply from NASEM 2021.} \label{nasemminkey} \\ +\caption{Key variables used in calculation of net energy supply from NASEM 2021.} \\ \toprule \multicolumn{1}{c}{\textbf{Variable}} & \multicolumn{1}{c}{\textbf{Description}} & @@ -2810,7 +2584,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in calculation of AA.} \label{nasemminkey} \\ +\caption{Key variables used in calculation of AA.} \\ \toprule \multicolumn{1}{c}{\textbf{Variable}} & \multicolumn{1}{c}{\textbf{Description}} & @@ -2866,7 +2640,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} \renewcommand{\arraystretch}{1.3} \begin{longtable}{@{} L{3.5cm} L{5.5cm} L{3.5cm} @{}} -\caption{Key variables used in calculation of AA.} \label{nasemminkey} \\ +\caption{Key variables used in calculation of AA.} \\ \toprule \multicolumn{1}{c}{\textbf{Variable}} & \multicolumn{1}{c}{\textbf{Description}} \\ @@ -2893,7 +2667,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} -\paragraph{AA Nutrient Supply} \label{aanutrient} +\paragraph{AA Nutrient Supply} This section is divided into several subsections including Rumen Degraded and Undegraded Protein, Dry Matter Intake, Dietary Nutrient Intake, Dietary Nutrient Concentration, Digested Nutrients, Digested Rumen Undegradable Protein (RUP), Microbial Nitrogen Growth, Ruminal Nitrogen Outflow, and lastly Amino Acid Supply. \vspace{0.2cm} @@ -3069,7 +2843,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} \end{center} \vspace{0.5cm} - {\raggedleft \textbf{[31]}\par} + {\raggedleft \textbf{[AN.SUP.31]}\par} \vspace{0.5cm} \textbf{ Mineral Supply} @@ -3111,8 +2885,7 @@ \subsubsection{Energy and Nutrition Supply }\label{sec:nutsupply} -\subsubsection{Automated Ration Formulation} \label{autoration} - +\subsubsection{Automated Ration Formulation} \paragraph{Introduction} Automated ration formulation in RuFaS optimizes a ration for a single objective (least cost), utilizing sequential least squares quadratic programming, as described in \cite{Li2022}. This process is carried out on an individual pen level, and uses the mean animal requirements and body weight during formulation. The ration formulation process includes information not only from the Animal Module’s inputs (Table RF1), but the primary Feed input file (Table RF2), and Feed ingredient inclusion rates defined in the Feed Storage module’s input files @@ -3121,85 +2894,67 @@ \subsubsection{Automated Ration Formulation} \label{autoration} -\renewcommand{\arraystretch}{1.4} % More vertical space between rows -\begin{longtable}{@{} L{5cm} L{7cm} C{2cm} C{2cm} C{2cm} @{} } -\caption{Key inputs found in the animal input file.} \\ -\toprule -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ -\midrule -\endfirsthead +\begin{landscape} +\thispagestyle{empty} + +\begin{table}[h!] +\caption{Key inputs found in the animal input file.} +\centering +\renewcommand{\arraystretch}{1.4} + +\begin{tabular}{@{} L{5cm} L{7cm} C{2cm} C{2cm} C{2cm} @{}} -\multicolumn{5}{@{}l}{\textit{Table continued from previous page}} \\ \toprule -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ +\textbf{Variable} & \textbf{Definition} & \textbf{Default} & \textbf{Min} & \textbf{Max} \\ \midrule -\endhead -\midrule -\multicolumn{5}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot +ration.user\_input & User decision to use the user-defined ration formulation or the automated ration formulation methods (true or false, respectively). & TRUE & - & - \\ -\bottomrule -\endlastfoot - -ration.user\_input & User decision to use the user-defined ration formulation or the automated ration formulation methods (true or false, respectively). & TRUE & - & - \\ ration.formulation\_interval & Ration formulation interval (days). & 30 & 1 & - \\ + ration.phosphorus\_requirement\_buffer & Increase in phosphorus nutrient requirement in calculation of animal requirements (percentage). & 75 & 0 & - \\ -\end{longtable} -\vspace{0.2cm} +\bottomrule -\renewcommand{\arraystretch}{1.4} % More vertical space between rows +\end{tabular} +\end{table} -\begin{longtable}{@{} L{3.5cm} L{5.5cm} L{4.5cm} C{2cm} C{2cm} C{2cm} @{}} -\caption{Key inputs found in the feed input file.} \\ -\toprule -\multicolumn{1}{c}{\textbf{Section}} & -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ -\midrule -\endfirsthead +\end{landscape} + + +\begin{landscape} +\thispagestyle{empty} + +\begin{table}[h!] +\caption{Key inputs found in the feed input file.} +\centering +\renewcommand{\arraystretch}{1.4} + +\begin{tabular}{@{} L{3.5cm} L{5.5cm} L{4.5cm} C{2cm} C{2cm} C{2cm} @{}} \toprule -\multicolumn{1}{c}{\textbf{Section}} & -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ +\textbf{Section} & \textbf{Variable} & \textbf{Definition} & \textbf{Default} & \textbf{Min} & \textbf{Max} \\ \midrule -\endhead -\midrule -\multicolumn{6}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot + & calf\_feeds or growing\_feeds or close\_up\_feeds or lac\_cow\_feeds & Each section is comprised of a list of feeds (RuFaS Feed IDs). & - & - & - \\ -\bottomrule -\endlastfoot +\multirow{2}{*}{\textbf{purchased\_feeds}} + & purchased\_feed & RuFaS Feed ID & - & - & - \\ + & purchased\_feed\_cost & Price per feed (dollars/kg DM). & - & - & - \\ -- & calf\_feeds or growing\_feeds or close\_up\_feeds or lac\_cow\_feeds & Each section is comprised of a list of feeds (RuFaS Feed IDs). & - & - & - \\ +\cmidrule(lr){1-6} -\multirow{2}{*}{\textbf{purchased\_feeds}} -& purchased\_feed & RuFaS Feed ID & - & - & - \\ -& purchased\_feed\_cost & Price per feed (dollars/kg DM). & - & - & - \\ +\multirow{3}{*}{\parbox{3cm}{\textbf{User\_defined\_ration\_percentages}}} + & calves/growing/close\_up/lac\_cow.ration\_percentage & For each feed ID, amount of a ration that is a given feed (percentage). & - & 0 & 100 \\ + & tolerance & Allowable +/- percentage variance in each of the defined ration inclusion percentage values (fraction). & 0.1 & 0 & 1 \\ + & milk\_reduction\_maximum & Allowable amount of milk reduction (kg) when dietary nutrient supply cannot meet animal requirements. & 15 & 0 & 50 \\ -\multirow{3}{*}{\textbf{User\_defined\_ration\_percentages}} -& calves/growing/close\_up/lac\_cow.ration\_percentage & For each feed ID, amount of a ration that is a given feed (percentage). & - & 0 & 100 \\ -& tolerance & Allowable +/- percentage variance in each of the defined ration inclusion percentage values (fraction). & 0.1 & 0 & 1 \\ -& milk\_reduction\_maximum & Allowable amount of milk reduction (kg) when dietary nutrient supply cannot meet animal requirements. & 15 & 0 & 50 \\ +\bottomrule -\end{longtable} +\end{tabular} +\end{table} + +\end{landscape} @@ -3271,8 +3026,6 @@ \subsubsection{Automated Ration Formulation} \label{autoration} The generalized equation for sequential quadratic programming is as follows \parencite{Li2022} and gi(x) is constraint i, which must be twice continuously differentiable with respect to all xj in x.”). -\textbf{\large INSERT EQUATION HERE} - \renewcommand{\arraystretch}{1.4} % More vertical space between rows @@ -3325,54 +3078,45 @@ \subsubsection{Automated Ration Formulation} \label{autoration} \subsubsection{User-defined ration formulation} +\vspace{0.3cm} + \paragraph{Introduction} -The user-defined ration methodology follows the same process as described in the Automated ration formulation methodology, with the addition of the inputs found in Table RF4, as described in the Methodology below. +The user-defined ration methodology follows the same process as described in the Automated ration formulation methodology, with the addition of the inputs found in this section, as described in the Methodology below. \textbf{Required User Inputs} -\renewcommand{\arraystretch}{1.4} % More vertical space between rows +\begin{landscape} +\thispagestyle{empty} -\begin{longtable}{@{} L{3.5cm} L{5.5cm} L{4.5cm} C{2cm} C{2cm} @{}} -\caption{Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages} \\ -\toprule +\begin{table}[h!] +\caption{Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages.} +\centering +\renewcommand{\arraystretch}{1.4} -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ -\midrule -\endfirsthead +\begin{tabular}{@{} L{3.5cm} L{5.5cm} L{4.5cm} C{2cm} C{2cm} @{}} \toprule - -\multicolumn{1}{c}{\textbf{Variable}} & -\multicolumn{1}{c}{\textbf{Definition}} & -\multicolumn{1}{c}{\textbf{Default}} & -\multicolumn{1}{c}{\textbf{Min}} & -\multicolumn{1}{c}{\textbf{Max}} \\ -\midrule -\endhead - +\textbf{Variable} & \textbf{Definition} & \textbf{Default} & \textbf{Min} & \textbf{Max} \\ \midrule -\multicolumn{5}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot - -\bottomrule -\endlastfoot calves or growing or close\_up or lac\_cow.ration\_percentage & For each feed ID, amount of a ration that is a given feed (percentage). & & 0 & 100 \\ + tolerance & Allowable +/- percentage variance in each of the defined ration inclusion percentage values (fraction). & 0.1 & 0 & 1 \\ + milk\_reduction\_maximum & Allowable amount of milk reduction (kg) when dietary nutrient supply cannot meet animal requirements. & 15 & 0 & 50 \\ +\bottomrule -\end{longtable} +\end{tabular} +\end{table} + +\end{landscape} \paragraph{Methodology} The key difference in the methodology for the user-defined ration methodology is that the feed inclusion rates are bounded by the user\_defined\_ration\_percentage values defined for each feed item (Table RF4). Those percentage values become the minimum and maximum inclusion value for each feed, with +/- the tolerance value (Table RF4) as a fraction of the percentage. -The ration formulation will proceed as described in the \hyperref[autoration]{Automated Methodology} above, but when formulation fails, different outcomes will occur. +The ration formulation will proceed as described in the Automated Methodology above, but when formulation fails, different outcomes will occur. \textit{For lactating cow pens} @@ -3541,23 +3285,7 @@ \subsection{Herd Size Management} - - - - - - - - - - - - - - - -\section{Animal-level Processes and Management}\label{sec:AnManage} - +\section{Animal-level Processes and Management} The methods in the RuFaS model that simulate individual animals’ life events and the effects of herd management on individual animals are referred to as the Animal Life Cycle Sub-module. This part of the model is driven by a Monte Carlo stochastic process that simulates the growth, production, reproduction, and culling of individual dairy cattle animals and shares aggregated outcomes with the Herd Management Sub-Module to manage herd dynamics on a daily basis. The life cycle module represents the variation in animal performance through the use of Monte Carlo Simulation methods \parencite{reuven2017}. Monte Carlo simulation relies on random draws from probability distributions rather than assigning fixed values. In this model, two main strategies are used: @@ -3572,7 +3300,7 @@ \section{Animal-level Processes and Management}\label{sec:AnManage} \paragraph{Flow of information} -For each animal object, the daily updates are called according to the order described in the \hyperref[sec:ADAY]{Day in the Life for Animal} on a RuFaS Farm. This is: +For each animal object, the daily updates are called according to the order described in the \hyperref{rufasday}{Day in the Life for Animal} on a RuFaS Farm. This is: \setlength{\parskip}{1em} \setlength{\parindent}{0pt} DigestiveSystem $\rightarrow$ NutrientInputs $\rightarrow$ MilkProduction $\rightarrow$ BodyweightChange $\rightarrow$ Reproduction $\rightarrow$ LifeStage Change $\rightarrow$ Parturition @@ -3593,7 +3321,7 @@ \section{Animal-level Processes and Management}\label{sec:AnManage} \centering \includegraphics[width=0.9\textwidth]{resources/animalgroups.png} % Replace with your image file \caption{There are 5 life stages from calf to cow and a cull stage as outlined in this figure.} - \label{fig:example} + \end{figure} \textbf{Progression Between Life Stages:} Calves progress to Heifer I when their age reaches the user-defined input for weaning day. Heifer I animals progress to Heifer II animals when their age reaches the user-defined input for breeding start day. Heifer II animals that successfully conceive progress to the Heifer III stage when they are close to calving. Specifically, Heifers II become Heifers III when the number of days left in their pregnancy is equal to the user-defined input for the prefresh days. When a Heifer III animal calves for the first time, she becomes a Cow and will remain a cow for the rest of her life on the RuFaS farm. @@ -3615,7 +3343,7 @@ \subsection{RuFaS Bodyweight and Growth} These methods are further described by \textcite{Li2023} -\textbf{Required User Inputs} \label{ANbwinputs} +\textbf{Required User Inputs} \renewcommand{\arraystretch}{1.4} \begin{longtable}{@{} L{4cm} L{6.5cm} L{1.5cm} L{1cm} L{1cm} @{}} @@ -3656,8 +3384,7 @@ \subsection{RuFaS Bodyweight and Growth} target\_heifer\_preg\_day & The target age (in days) for heifers to become pregnant - for adjusting heifer body weight (days) & 420 & NA & NA \\ \end{longtable} -\textbf{Expected Outputs} \label{ANbwoutputs} - +\textbf{Expected Outputs} \begin{itemize} \item herd\_statistics.avg\_cow\_body\_weight (kg): the daily average bodyweight of all cows in the herd \item Pen\_[pen ID]\_[pen animal combination].avg\_BW (kg): the daily average bodyweight of all animals in each pen @@ -3885,7 +3612,7 @@ \subsection{RuFaS Bodyweight and Growth} -\subsection{Animal Reproduction} \label{REPRO} +\subsection{Animal Reproduction} \paragraph{Introduction} The reproduction component of the RuFaS model is designed based on reproductive program options recommended by the Dairy Cattle Reproduction Council \parencite{dcrc_protocols} and experts in the field. It offers three pre-defined reproductive program options for nulliparous heifers (estrus detection [ED], timed artificial insemination [TAI], and synchronized estrus detection [Synch-ED]) and three options for lactating cows (ED, TAI, and a combined ED-TAI approach). Users can select appropriate reproductive protocols and specify reproductive performance variables for both nulliparous heifers and lactating cows. @@ -4032,8 +3759,7 @@ \subsection{Animal Reproduction} \label{REPRO} \item Updates to Protocols \end{itemize} - \paragraph{Methodology} \label{repromethod} - + \paragraph{Methodology} \textbf{\textit{Heifer Breeding}} \vspace{0.2cm} @@ -4042,7 +3768,7 @@ \subsection{Animal Reproduction} \label{REPRO} \centering \includegraphics[width=0.7\textwidth]{resources/repromethod.png} % Replace with your image file \caption{This is a high level schematic to illustrate the methodology behind the heifer breeding and re-breeding in RuFaS Animal Module.} - \label{fig:example} + \end{figure} Pregnancy diagnosis and reconfirmation occur after each insemination [heifer\_pregnancy\_update]. If a heifer remains nonpregnant beyond a user-defined age threshold (heifer\_repro\_cull\_time, e.g., 500 days), she is culled due to reproductive failure. At a user-defined day in pregnancy (prefresh\_day, e.g., one month before calving), the animal either transitions to the Heifer III stage or is sold as a replacement heifer. \vspace{0.2cm} @@ -4062,7 +3788,7 @@ \subsection{Animal Reproduction} \label{REPRO} \centering \includegraphics[width=0.75\textwidth]{resources/cowbreedmethod.png} \caption{This is a high level schematic to illustrate the methodology behind the cow breeding and re-breeding in RuFaS Animal Module.} - \label{fig:example} + \end{figure} @@ -4158,12 +3884,12 @@ \subsection{Animal Reproduction} \label{REPRO} \end{landscape} -\subsection{Milk Production} \label{milkprod} +\subsection{Milk Production} \paragraph{Introduction} This section describes how RuFaS determines the amount of milk and milk components produced by a particular cow on a particular day. \vspace{0.25cm} - Milk yield is largely determined by lactation curve parameters. Wood’s curve is the only lactation model implemented in RuFaS currently, but there is flexibility to potentially include other models as well. At the beginning of the simulation, the herd is assigned distributions for the Wood’s curve parameters l, m, and n for each parity of cows (see more information in the \hyperref[lactcurve]{Lactation Curve } section). At the beginning of each new lactation, each cow is assigned a set of parameters for that lactation based on the herd’s distributions for her current parity. + Milk yield is largely determined by lactation curve parameters. Wood’s curve is the only lactation model implemented in RuFaS currently, but there is flexibility to potentially include other models as well. At the beginning of the simulation, the herd is assigned distributions for the Wood’s curve parameters l, m, and n for each parity of cows (see more information in the Lactation Curve section). At the beginning of each new lactation, each cow is assigned a set of parameters for that lactation based on the herd’s distributions for her current parity. \vspace{0.25cm} When the cow starts lactating, she produces milk from the calving day until dry or culled according to the assigned lactation curve model. Each day, each cow’s milk production is calculated and recorded. Milk production is calculated from the Wood’s curve equation using the given lactation curve parameters and days in milk, and then adjusted by applying random variation and any milk reduction required by other parts of the model. Milk components (protein, fat, and lactose) are calculated based on milk production and percent of each component for each cow. @@ -4393,7 +4119,7 @@ \subsection{Milk Production} \label{milkprod} \textit{Parameters and Equations} \vspace{0.1cm} - These are comprehensively outlines in the \hyperref[lactcurve]{Lactation Curve Parameters Determination} Section. + These are comprehensively outlines in the Lactation Curve Parameters Determination Section. \vspace{0.1cm} LactationCurve.set\_lactation\_parameters() is called by: @@ -4596,7 +4322,7 @@ \subsection{Milk Production} \label{milkprod} \begin{tcolorbox}[colback=white, colframe=black, boxrule=0.5pt, arc=3pt, width=\textwidth] - For more information, refer to the \hyperref[REPRO]{Reproduction} section of this document. + For more information, refer to the Reproduction section of this document. \end{tcolorbox} \vspace{0.2cm} @@ -4604,18 +4330,18 @@ \subsection{Milk Production} \label{milkprod} \vspace{0.2cm} \begin{tcolorbox}[colback=white, colframe=black, boxrule=0.5pt, arc=3pt, width=\textwidth] - For more details on milk changes and reductions, go to the \hyperref[myprodred]{Milk Production and Reduction} portion of this section. . + For more details on milk changes and reductions, go to the Milk Production and Reduction portion of this section. . \end{tcolorbox} \end{enumerate} -\subsection{Lactation Curve: Parameters and Definitions} \label{lactcurve} +\subsection{Lactation Curve: Parameters and Definitions} \paragraph{Introduction} The Lactation Curve Parameter Determination module calculates and adjusts Wood’s lactation curve parameters (l, m, n) based on farm-specific attributes such as geographic location, management practices, and production levels. These parameters shape the milk production curve for cows across different parities (1st, 2nd, 3rd + lactations). - This module is part of the Animal Module and integrates with the \hyperref[milkprod]{Milk Production} calculations. The outputs influence various downstream models, including nutrient requirements, manure excretion, and greenhouse gas emission calculations. + This module is part of the Animal Module and integrates with the Milk Production calculations. The outputs influence various downstream models, including nutrient requirements, manure excretion, and greenhouse gas emission calculations. The primary class in this module is: @@ -4958,7 +4684,7 @@ \subsection{Lactation Curve: Parameters and Definitions} \label{lactcurve} \end{enumerate} - Equations below are not in the LactationCurve class, but they are useful to understanding the bigger picture of how lactation curve parameter estimates are generated in RuFaS. Please see the \hyperref[milkprod]{Milk Production} section for more details on these equations \parencite{Wood1967}. + Equations below are not in the LactationCurve class, but they are useful to understanding the bigger picture of how lactation curve parameter estimates are generated in RuFaS. Please see the Milk Production section for more details on these equations \parencite{Wood1967}. \vspace{0.5cm} \textbf{Wood's Lactation Curve} @@ -4992,7 +4718,7 @@ \subsection{Lactation Curve: Parameters and Definitions} \label{lactcurve} \vspace{0.5cm} -\subsection{Culling} \label{herdexit} +\subsection{Culling} \paragraph{Introduction} This section describes the processes of animals leaving the herd in RuFaS. @@ -5029,7 +4755,7 @@ \subsection{Culling} \label{herdexit} \thispagestyle{empty} % Suppress headers and footers on this landscape page \renewcommand{\arraystretch}{1.4} % More vertical space between rows -\begin{longtable}{@{} L{4cm} L{8cm} C{2cm} C{2cm} C{2cm} @{}} +\begin{longtable}{@{} L{6cm} L{12cm} C{2cm} C{2cm} C{2cm} @{}} \caption{The following inputs are used to determine the probability and timing of cow death and sales events.} \\ \toprule \textbf{Variable} & \textbf{Definition} & \textbf{Default} & \textbf{Min} & \textbf{Max} \\ @@ -5067,8 +4793,6 @@ \subsection{Culling} \label{herdexit} % <-- Ensure there's a final newline before closing the table \end{longtable} -\vspace{0.2cm} - {\footnotesize \textit{Note:} Variables marked with \textsuperscript{*} are commonly left at default values. Adjusting them changes the timing of cow exit from the herd but does not affect the total number of exits.} \end{landscape} @@ -5357,14 +5081,14 @@ \subsection{Manure Excretion} The Manure Excretion Calculator module computes manure excretion metrics for various animal categories. Inputs are drawn from pen ration files and animal module constants. They are organized into the following groups: \begin{enumerate} - \item \hyperref[ANgeneralmanexcinputs]{General Animal Inputs} - \item \hyperref[ANcowspecinputs]{Cow Specific Inputs} - \item \hyperref[ANPinputs]{Phosphorus Specific Inputs} + \item General Animal Inputs + \item Cow Specific Inputs + \item Phosphorus Specific Inputs \end{enumerate} % Begin longtable -\textbf{General Inputs} Manure Excretion \label{ANgeneralmanexcinputs} +\textbf{General Inputs} Manure Excretion \renewcommand{\arraystretch}{1.4} % More vertical space between rows \begin{longtable}{@{} L{5cm} p{7cm} C{3cm} @{}} @@ -5406,7 +5130,7 @@ \subsection{Manure Excretion} % Cow Specific Inputs Table % -------------------------- -\textbf{\large Cow Specific Inputs – Manure Excretion} \label{ANcowspecinputs} +\textbf{\large Cow Specific Inputs – Manure Excretion} \renewcommand{\arraystretch}{1.4} \begin{longtable}{@{} L{4.5cm} p{4.5cm} C{2cm} C{1cm} C{1cm} @{}} @@ -5445,7 +5169,7 @@ \subsection{Manure Excretion} % Phosphorus Excretion Inputs Table % -------------------------- -\textbf{\large Phosphorus Excretion Inputs – Manure Excretion} \label{ANPinputs} +\textbf{\large Phosphorus Excretion Inputs – Manure Excretion} \renewcommand{\arraystretch}{1.4} \begin{longtable}{@{} L{5cm} p{7cm} C{3cm} @{}} @@ -5484,7 +5208,7 @@ \subsection{Manure Excretion} \renewcommand{\arraystretch}{1.4} % More vertical space between rows \begin{longtable}{@{} C{3cm} C{3cm} C{5cm} C{1cm} @{}} -\caption{Expected outputs from this section.} \label{ANoutputes} \\ +\caption{Expected outputs from this section.} \\ \toprule \textbf{Category} & \textbf{Parameter} & \textbf{Definition} & \textbf{Units} \\ \midrule @@ -6263,7 +5987,7 @@ \subsection{Enteric Methane Emission} \renewcommand{\arraystretch}{1.4} % More vertical space between rows \begin{longtable}{@{} C{3cm} C{3cm} C{5cm} C{1cm} @{} } -\caption{Expected outputs from this section.} \label{ANoutputes} \\ +\caption{Expected outputs from this section.} \\ \toprule \textbf{Category} & \textbf{Parameter} & \textbf{Definition} & \textbf{Units} \\ @@ -6501,35 +6225,36 @@ \subsection{Enteric Methane Mitigation} \vspace{0.2cm} % --- Additive Dosage Table --- -\begin{longtable}{@{} L{3cm} p{5cm} C{5cm} @{}} -\caption{Dosage of methane mitigation additives.} \\ +\begin{longtable}{@{}L{3.3cm} L{6.7cm} L{5.0cm}@{}} +\caption{Dosage of methane mitigation additives.}\\ \toprule -\textbf{Variable Name} & \textbf{Definition} & \textbf{Default and Range} \\ +\textbf{Variable name} & \textbf{Definition} & \textbf{Default and range} \\ \midrule \endfirsthead -\multicolumn{3}{@{}l}{\textit{Table continued from previous page}} \\ +\multicolumn{3}{@{}l}{\textit{Table \thetable\ continued from previous page}}\\ \toprule -\textbf{Variable Name} & \textbf{Definition} & \textbf{Default and Range} \\ +\textbf{Variable name} & \textbf{Definition} & \textbf{Default and range} \\ \midrule \endhead \midrule -\multicolumn{3}{@{}r@{}}{\textit{Continued on next page}} \\ +\multicolumn{3}{@{}r@{}}{\textit{Continued on next page}}\\ \endfoot \bottomrule \endlastfoot -methane\_mitigation\_additive\_amount & Dosage per kg of DMI & 3-NOP: 70 (40–100); Monensin: 24 (20–36) mg/kg DMI \\ +methane_mitigation_additive_amount & +Dosage per kg of dry matter intake (DMI). & +3-NOP: 70 (40--100)\,mg/kg DMI; Monensin: 24 (20--36)\,mg/kg DMI \\ \end{longtable} -\vspace{0.3cm} % --- Expected Outputs Table --- \renewcommand{\arraystretch}{1.4} \begin{longtable}{@{} C{3cm} C{6cm} C{2cm} @{}} -\caption{Expected outputs from this section.} \label{ANoutputes} \\ +\caption{Expected outputs from this section.} \\ \toprule \textbf{Parameter} & \textbf{Definition} & \textbf{Units} \\ \midrule @@ -6609,103 +6334,6 @@ \subsection{Enteric Methane Mitigation} \end{itemize} -\newpage -\section{Abbreviations} - -\renewcommand{\arraystretch}{1.3} -\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}} - -\begin{longtable}{@{} L{4cm} L{12cm} @{}} -\caption{Common abbreviations used throughout this document} \\ - -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endfirsthead - -\multicolumn{2}{@{}l}{\textit{Table continued from previous page}} \\ -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endhead - -\midrule -\multicolumn{2}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot - -\bottomrule -\endlastfoot - -ADF & Acid detergent fiber (\% of DM) \\ -ADG & Average daily weight gain (g/d) \\ -Age1stBred & First breeding age (month) \\ -BCS5 & Body condition score (1–5 basis) \\ -BW & Body weight (kg) \\ -Ca & Calcium content (\% of DM) \\ -CBW & Calf birth weight (kg) \\ -CI & Calving interval (d) \\ -cm & centimeter \\ -Cost & Feed cost (\$/kg of DM) \\ -CP & Crude protein (\% of DM) \\ -d & days \\ -DE & Digestible energy (standard value, Mcal/kg) \\ -DIM & Days in milk \\ -DM & Dry matter (\% of as-fed basis) \\ -DMI & Dry matter intake \\ -DOP & Days of pregnancy (d) \\ -dRUP & RUP degradability (\% of RUP) \\ -EE & Ether extract, in crude fat (\% DM) \\ -EndCP & Endogenous CP \\ -EndN & Endogenous N \\ -EQSBW & Equivalent shrunk body weight (kg) \\ -FA & Fatty acids \\ -FIPS & Federal Information Processing Standards \\ -g & grams \\ -GE & Gross energy (standard value, Mcal/kg) \\ -GrUterW & Gravid uterine weight (kg) \\ -Kd & Rumen protein degradation rate (\%/h) \\ -kg & kilograms \\ -kJ & kilojoule \\ -L & liters \\ -m & meter \\ -max & maximum \\ -Mcal & Megacalorie \\ -MCP & Microbial Crude Protein \\ -ME & Metabolizable energy (standard value, Mcal/kg) \\ -MICP & Microbial CP \\ -min & minimum \\ -mL & milliliters \\ -MN & Microbial N \\ -MP & Metabolizable protein \\ -MTP & Microbial TP \\ -MW & Mature body weight (kg) \\ -MY & Milk yield \\ -N & Nitrogen (\% of DM) \\ -NASEM & National Academies of Sciences, Engineering, and Medicine \\ -NDF & Neutral detergent fiber (\% of DM) \\ -NEG & Net energy for growth (standard value, Mcal/kg) \\ -NEL & Net energy for lactation (standard value, Mcal/kg) \\ -NEM & Net energy for maintenance (standard value, Mcal/kg) \\ -nNDF & Nondigestible Neutral Detergent Fiber \\ -NPN & Non-protein Nitrogen \\ -NRC & National Research Council (updated in 2021 to NASEM) \\ -OM & Organic matter (\% of DM) \\ -P & Phosphorus content (\% of DM) \\ -PAF & Processing adjustment factor (not used) \\ -Parity & Number of lactations \\ -PrevTemp & Average daily temperature of last month (°C) \\ -RDP & Ruminally degraded CP \\ -ROM & Residual OM (\% of DM) \\ -RUP & Ruminally undegraded CP \\ -s & seconds \\ -TAN & Total ammoniacal N \\ -TDN & Total digestible nutrient (\% of DM) \\ -TP & True protein (\% of DM) \\ -USDA & United States Department of Agriculture \\ -UterW & Uterine weight (kg) \\ -WSC & Water Soluble Carbohydrates \\ -\end{longtable} - @@ -6716,4 +6344,3 @@ \section{References} \printbibliography[heading=subbibliography,title={ }] \end{refsection} -\end{document} diff --git a/docs/scientific/animalmoddoc.aux b/docs/scientific/animalmoddoc.aux new file mode 100644 index 0000000000..2e0909cff4 --- /dev/null +++ b/docs/scientific/animalmoddoc.aux @@ -0,0 +1,243 @@ +\relax +\providecommand\babel@aux[2]{} +\@nameuse{bbl@beforestart} +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\catcode 95\active +\abx@aux@refcontext{nyt/global//global/global} +\@writefile{toc}{\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{}} +\@writefile{toc}{\etoc@setlocaltop \Etoc@part@@ } +\babel@aux{english}{} +\@input{animal.aux} +\abx@aux@refsection{1}{6} +\abx@aux@cite{1}{reuven2017} +\abx@aux@segm{1}{0}{reuven2017} +\abx@aux@page{2}{6} +\abx@aux@cite{1}{Li2022} +\abx@aux@segm{1}{0}{Li2022} +\abx@aux@cite{1}{nrc2021} +\abx@aux@segm{1}{0}{nrc2021} +\abx@aux@cite{1}{nrc2001} 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Li2022 + reuven2017 + Li2023 + nrc2001 + Korver1985 + Galvao2013 + dcrc_protocols + devries2006 + kalantari2015using + wiltbank2016 + wiltbank2016 + Li2022 + Li2022 + Li2022 + Li2022 + Wood1967 + Hanson2024 + reed2015 + nennich2005 + asabe2005 + johnson2016 + appuhamy2014 + appuhamy2018 + vadas2007 + nrc2001 + nrc2021 + wilkerson1997prediction + boadi2004 + deboer2002a + monteny2002b + IPCC2006 + Mills2003 + Niu2018 + Pattanaik2003 + Pattanaik2003 + Niu2018 + Niu2018 + Mills2003 + Niu2018 + Mills2003 + Niu2018 + Kebreab2023 + + + + + + + + presort + + + sortkey + + + sortname + author + editor + translator + sorttitle + title + + + sortyear + year + + + sorttitle + title + + + volume + 0 + + + + + + diff --git a/docs/scientific/animalmoddoc.blg b/docs/scientific/animalmoddoc.blg new file mode 100644 index 0000000000..8fb9b831cb --- /dev/null +++ b/docs/scientific/animalmoddoc.blg @@ -0,0 +1,17 @@ +[0] Config.pm:307> INFO - This is Biber 2.19 +[0] Config.pm:310> INFO - Logfile is 'animalmoddoc.blg' +[137] biber-MSWIN64:340> INFO - === +[179] Biber.pm:419> INFO - Reading 'animalmoddoc.bcf' +[305] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[316] Biber.pm:979> INFO - Found 29 citekeys in bib section 1 +[316] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[338] Biber.pm:4419> INFO - Processing section 1 +[353] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1 +[401] bibtex.pm:1713> INFO - LaTeX decoding ... +[480] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib' +[718] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[719] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[719] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[719] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[764] bbl.pm:660> INFO - Writing 'animalmoddoc.bbl' with encoding 'UTF-8' +[794] bbl.pm:763> INFO - Output to animalmoddoc.bbl diff --git a/docs/scientific/animalmoddoc.fdb_latexmk b/docs/scientific/animalmoddoc.fdb_latexmk new file mode 100644 index 0000000000..9772cfa100 --- /dev/null +++ b/docs/scientific/animalmoddoc.fdb_latexmk @@ -0,0 +1,298 @@ +# Fdb version 4 +["biber animalmoddoc"] 1773835560.74045 "animalmoddoc.bcf" "animalmoddoc.bbl" "animalmoddoc" 1773836218.08485 0 + "animalmoddoc.bcf" 1773836216 112259 a9526a3fa13d06622e8c4a1f0455c20c "pdflatex" + "resources/animal.bib" 1773235466 19843 003ce6dc3163a9c1fd885dbc082d404e "" + (generated) + "animalmoddoc.bbl" + "animalmoddoc.blg" + (rewritten before read) +["pdflatex"] 1773836210.18723 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/animalmoddoc.tex" "animalmoddoc.pdf" "animalmoddoc" 1773836218.08629 0 + "C:/Program Files/MiKTeX/tex/latex/listings/lstpatch.sty" 1763898348 353 9024412f43e92cd5b21fe9ded82d0610 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{table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{7}{table.1}% +\contentsline {table}{\numberline {2}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section}}{8}{table.2}% +\contentsline {table}{\numberline {3}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section.}}{8}{table.3}% +\contentsline {table}{\numberline {4}{\ignorespaces The user must define at least 3 pens and for each pen, key inputs are:}}{12}{table.4}% +\contentsline {table}{\numberline {6}{\ignorespaces A summary of animal types}}{13}{table.caption.2}% +\contentsline {table}{\numberline {7}{\ignorespaces Key variables used in protein requirement calculations.}}{20}{table.7}% +\contentsline {table}{\numberline {8}{\ignorespaces Key variables used in mineral requirement calculations.}}{23}{table.8}% +\contentsline {table}{\numberline {9}{\ignorespaces Key variables used in DMI requirement calculations.}}{24}{table.9}% +\contentsline {table}{\numberline {10}{\ignorespaces Key variables used in protein requirement calculations.}}{30}{table.10}% +\contentsline {table}{\numberline {11}{\ignorespaces Key variables used in mineral requirement calculations.}}{33}{table.11}% +\contentsline {table}{\numberline {12}{\ignorespaces Key variables used in DMI estimation calculations.}}{35}{table.12}% +\contentsline {table}{\numberline {13}{\ignorespaces Essential and non-essential amino acids}}{35}{table.13}% +\contentsline {table}{\numberline {14}{\ignorespaces Key variables used in calculation of AA.}}{37}{table.14}% +\contentsline {table}{\numberline {15}{\ignorespaces Key variables used in calculation of net energy in NRC 2001.}}{41}{table.15}% +\contentsline {table}{\numberline {16}{\ignorespaces Key variables used in calculation of net energy supply from NASEM 2021.}}{43}{table.16}% +\contentsline {table}{\numberline {17}{\ignorespaces Key variables used in calculation of AA.}}{46}{table.17}% +\contentsline {table}{\numberline {18}{\ignorespaces Key variables used in calculation of AA.}}{46}{table.18}% +\contentsline {table}{\numberline {19}{\ignorespaces Key inputs found in the animal input file.}}{50}{table.19}% +\contentsline {table}{\numberline {20}{\ignorespaces Key inputs found in the feed input file.}}{50}{table.20}% +\contentsline {table}{\numberline {21}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{51}{table.21}% +\contentsline {table}{\numberline {22}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{52}{table.22}% +\contentsline {table}{\numberline {23}{\ignorespaces Below is a summary of the user inputs that are available and their definitions.}}{57}{table.23}% +\contentsline {table}{\numberline {24}{\ignorespaces Below are the key user inputs that determine the \textbf {heifer reproductive breeding program} and impact reproductive efficiency and age at first calving.}}{63}{table.caption.5}% +\contentsline {table}{\numberline {25}{\ignorespaces The following inputs determine reproductive efficiency of cows and influence culling, calving interval, and calf output.}}{64}{table.25}% +\contentsline {table}{\numberline {26}{\ignorespaces The following inputs can be used to determine if there is a \textbf {decrease in the conception rate} with parity and rebreeding attempts.}}{65}{table.caption.6}% +\contentsline {table}{\numberline {27}{\ignorespaces Important functions for the reproduction section.}}{71}{table.27}% +\contentsline {table}{\numberline {28}{\ignorespaces The following user inputs are used to estimate customized herd-level lactation curve parameters. See the Methodology section of this document and the Lactation Curve Scientific Documentation for more detail about how these inputs are used with relation to daily milk production.}}{74}{table.28}% +\contentsline {table}{\numberline {29}{\ignorespaces The following inputs are used to determine the milk fat and milk protein percentages for each lactating cow}}{75}{table.29}% +\contentsline {table}{\numberline {30}{\ignorespaces The following inputs are used to constrain how much an average cow’s daily milk production will be reduced due to an inadequate ration. See the Methodology section of this document and the Ration Formulation scientific documentation for more detail about how these inputs are used with relation to daily milk production.}}{76}{table.30}% +\contentsline {table}{\numberline {31}{\ignorespaces Wood's Lactation Curve Base Parameters – These inputs provide the baseline values and variability for Wood’s lactation curve parameters as derived from \blx@tocontentsinit {1}\textcite {Li2022}.}}{83}{table.31}% +\contentsline {table}{\numberline {33}{\ignorespaces Adjustment Factors – These factors adjust the base parameters based on geographical, temporal, management, and parity considerations.}}{84}{table.33}% +\contentsline {table}{\numberline {35}{\ignorespaces Farm Specific 305-Day Milk Production — These inputs help tailor the lactation curve to the farm’s production targets and herd composition.}}{85}{table.35}% +\contentsline {table}{\numberline {36}{\ignorespaces Summary of important functions for the reproduction section. }}{86}{table.36}% +\contentsline {table}{\numberline {37}{\ignorespaces The following inputs are used to determine the probability and timing of cow death and sales events.}}{90}{table.37}% +\contentsline {table}{\numberline {38}{\ignorespaces Cumulative distribution function (CDF) values associated with the conditional probability that a sold animal is removed due to each group of issues and/or the conditional probability of death over time. Corresponds to the “probability” value for each cull reason in the animal input json file. The 'cull\_day\_count' array defines the segments of the CDF}}{96}{table.caption.10}% +\contentsline {table}{\numberline {39}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{98}{table.39}% +\contentsline {table}{\numberline {40}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{98}{table.40}% +\contentsline {table}{\numberline {41}{\ignorespaces These inputs define phosphorus-related outputs relevant to lactating cows.}}{99}{table.41}% +\contentsline {table}{\numberline {42}{\ignorespaces Expected outputs from this section.}}{99}{table.42}% +\contentsline {table}{\numberline {43}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{109}{table.43}% +\contentsline {table}{\numberline {44}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{109}{table.44}% +\contentsline {table}{\numberline {45}{\ignorespaces Inputs specific to the methane emissions model and selected mitigation strategies.}}{110}{table.45}% +\contentsline {table}{\numberline {46}{\ignorespaces Expected outputs from this section.}}{110}{table.46}% +\contentsline {table}{\numberline {47}{\ignorespaces General dietary fiber and fat concentration inputs.}}{113}{table.47}% +\contentsline {table}{\numberline {48}{\ignorespaces Feed-based methane mitigation strategies.}}{113}{table.48}% +\contentsline {table}{\numberline {49}{\ignorespaces Dosage of methane mitigation additives.}}{114}{table.49}% +\contentsline {table}{\numberline {50}{\ignorespaces Expected outputs from this section.}}{114}{table.50}% diff --git a/docs/scientific/animalmoddoc.out b/docs/scientific/animalmoddoc.out new file mode 100644 index 0000000000..c7cdf67838 --- /dev/null +++ b/docs/scientific/animalmoddoc.out @@ -0,0 +1,24 @@ +\BOOKMARK 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file mode 100644 index 0000000000..d713fdfdcf --- /dev/null +++ b/docs/scientific/animalmoddoc.tex @@ -0,0 +1,33 @@ +\documentclass{article} + +\input{preamble} + +\begin{document} + + \thispagestyle{empty} + \centering + \vspace*{2cm} + + {\Huge\bfseries Animal Module\par} + \vspace{1cm} + + {\Large RuFaS Scientific Documentation\par} + \vspace{1cm} + + \includegraphics[width=0.5\textwidth]{resources/animal1.png} % Adjust size and filename + + \vfill + + {\small v.1\par} + \vspace*{1cm} + +\newpage + + +% Continue with front matter (e.g., table of contents) +\thispagestyle{fancy} % Ensure the header/footer appears on the first page + + +\include{animal} + +\end{document} \ No newline at end of file diff --git a/docs/scientific/animalmoddoc.toc b/docs/scientific/animalmoddoc.toc new file mode 100644 index 0000000000..fb2384dae3 --- /dev/null +++ b/docs/scientific/animalmoddoc.toc @@ -0,0 +1,130 @@ +\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{} +\etoc@setlocaltop \Etoc@part@@ +\babel@toc {english}{}\relax +\contentsline {part}{I\hspace {1em}Animal Module}{2}{part.1}% +\etoc@startlocaltoc {1} +\etoc@startlocaltoc {2} +\etoc@startlocaltoc {3} +\contentsline {section}{\numberline {1}Module Introduction}{6}{section.1}% +\contentsline {subsection}{\numberline {1.a}Animal Life Cycle}{6}{subsection.1.1}% +\contentsline {section}{\numberline {2}Herd-level Processes and Management}{7}{section.2}% +\contentsline {subsection}{\numberline {2.a}Herd Initialization}{7}{subsection.2.1}% +\contentsline {paragraph}{Introduction}{7}{subsection.2.1}% +\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{8}{table.1}% +\contentsline {table}{\numberline {2}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section}}{9}{table.2}% +\contentsline {table}{\numberline {3}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section.}}{9}{table.3}% +\contentsline {paragraph}{Methodology}{11}{table.3}% +\contentsline {subsection}{\numberline {2.b}Pens and Animal Grouping}{12}{subsection.2.2}% +\contentsline {paragraph}{Introduction}{12}{subsection.2.2}% +\contentsline {table}{\numberline {4}{\ignorespaces The user must define at least 3 pens and for each pen, key inputs are:}}{13}{table.4}% +\contentsline {paragraph}{Methodology}{14}{table.5}% +\contentsline {table}{\numberline {6}{\ignorespaces A summary of animal types}}{14}{table.caption.2}% +\contentsline {paragraph}{Remove\_animals\_by\_ids}{14}{table.caption.2}% +\contentsline {paragraph}{\_add\_new\_animals}{15}{table.caption.2}% +\contentsline {paragraph}{Set\_animal\_nutritional\_requirements}{15}{table.caption.2}% +\contentsline {subsection}{\numberline {2.c}Ration Formulation}{15}{subsection.2.3}% +\contentsline {subsubsection}{\numberline {2.c.i}Energy and Nutrition Requirements}{15}{subsubsection.2.3.1}% +\contentsline {paragraph}{NRC: Calculating Nutrient Requirements of Dairy Cattle}{15}{subsubsection.2.3.1}% +\contentsline {subsubsection}{\numberline {2.c.ii}Nutrient Requirements of Dairy Cattle (NRC)}{16}{subsubsection.2.3.2}% +\contentsline {table}{\numberline {7}{\ignorespaces Key variables used in protein requirement calculations.}}{21}{table.7}% +\contentsline {table}{\numberline {8}{\ignorespaces Key variables used in mineral requirement calculations.}}{24}{table.8}% +\contentsline {table}{\numberline {9}{\ignorespaces Key variables used in DMI requirement calculations.}}{25}{table.9}% +\contentsline {paragraph}{NASEM: Calculating Nutrient Requirements of Dairy Cattle: Eighth Revised Edition}{25}{table.9}% +\contentsline {table}{\numberline {10}{\ignorespaces Key variables used in protein requirement calculations.}}{31}{table.10}% +\contentsline {table}{\numberline {11}{\ignorespaces Key variables used in mineral requirement calculations.}}{34}{table.11}% +\contentsline {table}{\numberline {12}{\ignorespaces Key variables used in DMI estimation calculations.}}{36}{table.12}% +\contentsline {paragraph}{NASEM: Calculating Amino Acid Requirements}{36}{table.12}% +\contentsline {table}{\numberline {13}{\ignorespaces Essential and non-essential amino acids}}{36}{table.13}% +\contentsline {table}{\numberline {14}{\ignorespaces Key variables used in calculation of AA.}}{38}{table.14}% +\contentsline {subsubsection}{\numberline {2.c.iii}Energy and Nutrition Supply }{40}{subsubsection.2.3.3}% +\contentsline {paragraph}{Nutrient Supply}{40}{subsubsection.2.3.3}% +\contentsline {paragraph}{Energy Supply - NRC 2001}{40}{subsubsection.2.3.3}% +\contentsline {table}{\numberline {15}{\ignorespaces Key variables used in calculation of net energy in NRC 2001.}}{42}{table.15}% +\contentsline {paragraph}{Energy Supply - NASEM 2021}{42}{table.15}% +\contentsline {table}{\numberline {16}{\ignorespaces Key variables used in calculation of net energy supply from NASEM 2021.}}{44}{table.16}% +\contentsline {table}{\numberline {17}{\ignorespaces Key variables used in calculation of AA.}}{47}{table.17}% +\contentsline {table}{\numberline {18}{\ignorespaces Key variables used in calculation of AA.}}{47}{table.18}% +\contentsline {paragraph}{AA Nutrient Supply}{48}{table.18}% +\contentsline {subsubsection}{\numberline {2.c.iv}Automated Ration Formulation}{50}{subsubsection.2.3.4}% +\contentsline {paragraph}{Introduction}{50}{subsubsection.2.3.4}% +\contentsline {table}{\numberline {19}{\ignorespaces Key inputs found in the animal input file.}}{51}{table.caption.3}% +\contentsline {table}{\numberline {20}{\ignorespaces Key inputs found in the feed input file.}}{52}{table.caption.4}% +\contentsline {paragraph}{Methodology}{53}{table.caption.4}% +\contentsline {table}{\numberline {21}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{54}{table.21}% +\contentsline {subsubsection}{\numberline {2.c.v}User-defined ration formulation}{54}{subsubsection.2.3.5}% +\contentsline {paragraph}{Introduction}{54}{subsubsection.2.3.5}% +\contentsline {table}{\numberline {22}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages.}}{55}{table.caption.5}% +\contentsline {paragraph}{Methodology}{56}{table.caption.5}% +\contentsline {subsection}{\numberline {2.d}Herd Size Management}{56}{subsection.2.4}% +\contentsline {section}{\numberline {3}Animal-level Processes and Management}{58}{section.3}% +\contentsline {paragraph}{Flow of information}{58}{section.3}% +\contentsline {figure}{\numberline {1}{\ignorespaces There are 5 life stages from calf to cow and a cull stage as outlined in this figure.}}{59}{figure.caption.6}% +\contentsline {subsection}{\numberline {3.a}RuFaS Bodyweight and Growth}{59}{subsection.3.1}% +\contentsline {paragraph}{Introduction}{59}{subsection.3.1}% +\contentsline {table}{\numberline {23}{\ignorespaces Below is a summary of the user inputs that are available and their definitions.}}{60}{table.23}% +\contentsline {paragraph}{Methodology}{60}{table.23}% +\contentsline {paragraph}{Parity 1 Animals:}{62}{table.23}% +\contentsline {paragraph}{Parity 2 Animals}{62}{table.23}% +\contentsline {subsection}{\numberline {3.b}Animal Reproduction}{64}{subsection.3.2}% +\contentsline {paragraph}{Introduction}{64}{subsection.3.2}% +\contentsline {table}{\numberline {24}{\ignorespaces Below are the key user inputs that determine the \textbf {heifer reproductive breeding program} and impact reproductive efficiency and age at first calving.}}{66}{table.caption.8}% +\contentsline {table}{\numberline {25}{\ignorespaces The following inputs determine reproductive efficiency of cows and influence culling, calving interval, and calf output.}}{67}{table.25}% +\contentsline {table}{\numberline {26}{\ignorespaces The following inputs can be used to determine if there is a \textbf {decrease in the conception rate} with parity and rebreeding attempts.}}{68}{table.caption.9}% +\contentsline {paragraph}{Methodology}{69}{table.caption.9}% +\contentsline {figure}{\numberline {2}{\ignorespaces This is a high level schematic to illustrate the methodology behind the heifer breeding and re-breeding in RuFaS Animal Module.}}{70}{figure.caption.10}% +\contentsline {figure}{\numberline {3}{\ignorespaces This is a high level schematic to illustrate the methodology behind the cow breeding and re-breeding in RuFaS Animal Module.}}{72}{figure.caption.11}% +\contentsline {table}{\numberline {27}{\ignorespaces Important functions for the reproduction section.}}{74}{table.27}% +\contentsline {subsection}{\numberline {3.c}Milk Production}{76}{subsection.3.3}% +\contentsline {paragraph}{Introduction}{76}{subsection.3.3}% +\contentsline {table}{\numberline {28}{\ignorespaces The following user inputs are used to estimate customized herd-level lactation curve parameters. See the Methodology section of this document and the Lactation Curve Scientific Documentation for more detail about how these inputs are used with relation to daily milk production.}}{77}{table.28}% +\contentsline {table}{\numberline {29}{\ignorespaces The following inputs are used to determine the milk fat and milk protein percentages for each lactating cow}}{78}{table.29}% +\contentsline {table}{\numberline {30}{\ignorespaces The following inputs are used to constrain how much an average cow’s daily milk production will be reduced due to an inadequate ration. See the Methodology section of this document and the Ration Formulation scientific documentation for more detail about how these inputs are used with relation to daily milk production.}}{79}{table.30}% +\contentsline {paragraph}{Methodology}{80}{table.30}% +\contentsline {figure}{\numberline {4}{\ignorespaces A schematic illustrating the flow of milk reduction in ration formulation logic.}}{83}{figure.caption.12}% +\contentsline {subsection}{\numberline {3.d}Lactation Curve: Parameters and Definitions}{84}{subsection.3.4}% +\contentsline {paragraph}{Introduction}{84}{subsection.3.4}% +\contentsline {table}{\numberline {31}{\ignorespaces Wood's Lactation Curve Base Parameters – These inputs provide the baseline values and variability for Wood’s lactation curve parameters as derived from \blx@tocontentsinit {1}\textcite {Li2022}.}}{86}{table.31}% +\contentsline {table}{\numberline {33}{\ignorespaces Adjustment Factors – These factors adjust the base parameters based on geographical, temporal, management, and parity considerations.}}{87}{table.33}% +\contentsline {table}{\numberline {35}{\ignorespaces Farm Specific 305-Day Milk Production — These inputs help tailor the lactation curve to the farm’s production targets and herd composition.}}{88}{table.35}% +\contentsline {table}{\numberline {36}{\ignorespaces Summary of important functions for the reproduction section. }}{89}{table.36}% +\contentsline {paragraph}{Methodology}{89}{table.36}% +\contentsline {subsection}{\numberline {3.e}Culling}{91}{subsection.3.5}% +\contentsline {paragraph}{Introduction}{91}{subsection.3.5}% +\contentsline {table}{\numberline {37}{\ignorespaces The following inputs are used to determine the probability and timing of cow death and sales events.}}{93}{table.37}% +\contentsline {paragraph}{Methodology}{94}{table.37}% +\contentsline {table}{\numberline {38}{\ignorespaces Cumulative distribution function (CDF) values associated with the conditional probability that a sold animal is removed due to each group of issues and/or the conditional probability of death over time. Corresponds to the “probability” value for each cull reason in the animal input json file. The 'cull\_day\_count' array defines the segments of the CDF}}{98}{table.caption.13}% +\contentsline {section}{\numberline {4}Methane Emission and Manure Excretion}{99}{section.4}% +\contentsline {subsection}{\numberline {4.a}Manure Excretion}{99}{subsection.4.1}% +\contentsline {paragraph}{Introduction}{99}{subsection.4.1}% +\contentsline {table}{\numberline {39}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{100}{table.39}% +\contentsline {table}{\numberline {40}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{100}{table.40}% +\contentsline {table}{\numberline {41}{\ignorespaces These inputs define phosphorus-related outputs relevant to lactating cows.}}{101}{table.41}% +\contentsline {table}{\numberline {42}{\ignorespaces Expected outputs from this section.}}{101}{table.42}% +\contentsline {paragraph}{Methodology}{102}{table.42}% +\contentsline 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{45}{\ignorespaces Inputs specific to the methane emissions model and selected mitigation strategies.}}{112}{table.45}% +\contentsline {table}{\numberline {46}{\ignorespaces Expected outputs from this section.}}{112}{table.46}% +\contentsline {paragraph}{Methodology}{112}{table.46}% +\contentsline {paragraph}{Mutian Model}{113}{table.46}% +\contentsline {paragraph}{Mills Model}{114}{table.46}% +\contentsline {paragraph}{IPCC Model}{114}{table.46}% +\contentsline {paragraph}{Mills Model}{114}{table.46}% +\contentsline {paragraph}{IPCC Model}{114}{table.46}% +\contentsline {subsection}{\numberline {4.c}Enteric Methane Mitigation}{115}{subsection.4.3}% +\contentsline {paragraph}{Introduction}{115}{subsection.4.3}% +\contentsline {table}{\numberline {47}{\ignorespaces General dietary fiber and fat concentration inputs.}}{115}{table.47}% +\contentsline {table}{\numberline {48}{\ignorespaces Feed-based methane mitigation strategies.}}{115}{table.48}% +\contentsline {table}{\numberline 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-\usepackage{float} % Allows strict image placement -\usepackage[colorlinks=true, allcolors=blue]{hyperref}% hyperref makes the TOC clickable -\usepackage[most]{tcolorbox} -% Fonts -\usepackage[scaled]{helvet} -\renewcommand{\familydefault}{\sfdefault} -\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}} -\newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}} -\usepackage{pdflscape} % or \usepackage{lscape} -\usepackage{lipsum} % for dummy text -\usepackage{longtable} -\usepackage{caption} -\usepackage{multirow} -\usepackage{tocloft} % Customize LoT and LoF formatting -\usepackage{ragged2e} - -% Geometry -\usepackage[ - a4paper, - top=1.5in, - bottom=1in, - left=1in, - right=1in, - headheight=60pt, % This must match the vertical space used - headsep=20pt -]{geometry} - -% Define header and footer styles -% Fancy Header -\usepackage{fancyhdr} -\usepackage{rotating} -\pagestyle{fancy} -\fancyhf{} % clear all header/footer fields -\renewcommand{\headrulewidth}{0pt} % no horizontal line -% Header setup -\fancyhead[C]{% - \vspace{25pt} - \raisebox{15pt}[0pt][0pt]{% - \makebox[\textwidth]{% - \includegraphics[height=40pt]{resources/rufas.png}\hfill - \textbf{\today}% - } - }\\[-25pt] - \centering\textbf{Scientific Documentation of RuFaS Model} \\ - \rule{\textwidth}{1pt} -} - - -% Footer setup with a divider line and two lines of text on left and right -\renewcommand{\footrulewidth}{0.4pt} -\fancyfoot[L]{% - \begin{tabular}[t]{@{}l@{}} - Ruminant Farm System\\ - Sci Doc v.1 - \end{tabular}% -} -\fancyfoot[C]{\thepage} % Center: page number -\fancyfoot[R]{% - \begin{tabular}[t]{@{}r@{}} - \nouppercase{\leftmark}\\ % This pulls in the current section title - \end{tabular}% -} -% Landscape pages should be blank (no headers/footers) -\fancypagestyle{landscapeplain}{ - \fancyhf{} % clear all - \renewcommand{\headrulewidth}{0pt} - \renewcommand{\footrulewidth}{0pt} -} - - -% Bibliography setup -\usepackage[ - backend=biber, - style=authoryear, % You can change this to numeric, apa, etc. - natbib=true % Enables \citep, \citet if desired -]{biblatex} - -\addbibresource{resources/crop_and_soil.bib} % Your .bib file name -\usepackage{titlesec} -\usepackage{etoolbox} - -% Reset subsection counter at each new section -\pretocmd{\section}{\setcounter{subsection}{0}}{}{} - -% Roman for \section, Alpha for \section, alpha for \subsection -\renewcommand{\thesection}{\Roman{section}.} % I, II, III... -\renewcommand{\thesubsection}{\Alph{subsection}.} % A, B, C... -\renewcommand{\thesubsubsection}{\alph{subsubsection}.} % a, b, c... - -% --- Title Formats (in size order) --- -\titleformat{\section} - {\Large\bfseries} % Section: largest - {\thesection} % Label - {1em} % Spacing between label and title - {} % Before-code - -\titleformat{\subsection} - {\Large\bfseries} % Subsection: medium - {\thesubsection} - {1em} - {} - -\titleformat{\subsubsection} - {\normalsize\bfseries} % Subsubsection: smallest - {\thesubsubsection} - {1em} - {} - -% --- Spacing for each level --- -\titlespacing{\section}{0pt}{10pt plus 2pt minus 1pt}{5pt} -\titlespacing{\section}{0pt}{8pt plus 1pt minus 1pt}{4pt} -\titlespacing{\subsection}{0pt}{6pt plus 1pt minus 1pt}{3pt} - -% Optional: Keep your TOC control if needed -\usepackage{etoc} - -% Optional: If using headers/footers -\renewcommand{\sectionmark}[1]{\markboth{#1}{}} - - -% Remove default date from title -\date{} % Prevents date from appearing in \maketitle - - -% Define title -\title{\textbf{}} -\author{ } -\setlength{\topskip}{10pt} % Ensures LaTeX reserves room above the first line -%\usepackage{showframe} - -\begin{document} - -% Custom Title Page -\begin{titlepage} - \thispagestyle{empty} - \centering - \vspace*{2cm} - - {\Huge\bfseries Ruminant Farm System Model\par} - \vspace{1cm} - - {\Large Soil and Crop\par} - \vspace{1cm} - - {\large \today\par} - \vspace{1.5cm} % Add space before the image - - \includegraphics[width=0.25\textwidth]{resources/crop.png} % Adjust size and filename - - \vfill - - {\small v.1; Updated 2025\par} - \vspace*{1cm} -\end{titlepage} - - -\newpage - - -% Continue with front matter (e.g., table of contents) -\thispagestyle{fancy} % Ensure the header/footer appears on the first page - +\part{Soil and Crop Module} % Global Table of Contents \thispagestyle{fancy} -\tableofcontents -\newpage - -\listoffigures +% Local TOC that includes only what’s inside THIS section +\etocsettocstyle{\subsection*{Contents}}{} % heading for the local toc +\etocsetnexttocdepth{subsection} % or subsubsection +\localtableofcontents \newpage -\listoftables +\section*{List of Figures} +\locallistoffigures \newpage -% --- Global Structure --- -\section{Preface: A Day in the Life on a RuFaS Farm} - -This document provides a high-level overview of the daily operations of a ruminant farm, as modeled by RuFaS. The overview will be through the eyes of Dr. Rue Fas. One day, Dr. Rue woke up and decided the life of a computer scientist wasn’t for her. So she bought a dairy farm, and this is how she operates it every day. - -\paragraph{Feeding the Animals} -Second thing in the morning, after coffee, Dr. Rue checks the calendar to see if it’s time to formulate a new ration for her animals. -\vspace{0.2cm} - -If a new ration needs to be formulated, Dr. Rue heads over to the barn where she keeps all her forages and feed. While there, she checks how well all the forages are holding up. After considering the feeds available, the quality of each one, and how much each one costs, she decides on how productive she wants her animals to be. It is a difficult balancing act, but eventually a ration recipe is found that will keep the animals happy while keeping costs low and sustainability high until the calendar says the ration recipe needs to be reformulated. -\vspace{0.2cm} - -When Dr. Rue doesn’t need to formulate a new ration, she takes the last ration recipe she made and grabs all the feed and forage the animals need for the day out of the feed barn. If there isn’t enough for the animals, then a new ration is formulated using the steps above. - -\paragraph{Taking Care of the Animals} -After making sure all the animals’ feed is taken care of, Dr. Rue moves on to taking care of all the other animal tasks. This includes milking the animals, making sure they’re healthy, getting them pregnant, and numerous other tasks. -\vspace{0.2cm} - -As dawn breaks on the RuFaS farm, the animals awaken after a restful night. Joe, the farm master, prepares a large whiteboard to track HerdReproductionStatistics, ensuring he has all the data he needs for the day’s activities. - -\textit{Daily Routine} - After leaving their pens, each animal lines up in front of the barn. Julie, the diligent farm veterinarian, examines them one by one. This daily check includes updates on the following areas: -\begin{itemize} - \item Nutrients: Each animal begins its day with a quick phosphorus requirement assessment. Julie records these details and updates the animal’s phosphorus-related metrics. - \item Digestive System: With nutrient information in hand, Julie shifts focus to each animal’s digestive system, estimating manure output and enteric methane production for that day. - - \item Milk Production: All milking cows are assessed to gauge daily milk yield and milk component content (fat and protein). Any necessary adjustments are noted. - - \item Animal Growth: Around midday, Julie returns to each animal to evaluate daily weight changes. She updates each animal’s body weight accordingly. - - \item Reproduction: HeiferII and Cow stage animals undergo a reproduction check. Julie closely monitors their reproductive progress and updates the HerdReproductionStatistics details on Joe’s whiteboard. - - \item Life Stage Evaluation: Once the daily routines are complete, Julie determines if any animal is ready to progress to the next life stage. Graduating animals are marked as “graduated” to be moved to their new pens. Animals that must leave the herd—due to health, productivity, or other issues—are labeled as “sold” or “dead” to be removed from the farm population. - - \item Herd Size Maintenance: After every animal has been evaluated, Joe counts the herd to ensure it remains at a healthy size. If it is too large, he arranges the sale of some animals. If the herd is too small, he may opt to purchase additional heiferIIIs to keep numbers at the ideal level. - - \item Herd Structure Management: Joe also manages pen assignments. Newly graduated or newborn animals are guided to suitable pens, while animals marked for removal (sold or deceased) are taken out of the herd and removed from the farm records. -\end{itemize} - - -\textit{Output Reporting} -At day’s end, Joe and Julie review the updated HerdReproductionStatistics on the whiteboard. Joe then compiles a concise report summarizing the day’s herd stats. He forwards this information to the OutputManager before wrapping up another successful day on the RuFaS farm. -\vspace{0.5cm} - -\paragraph{Dealing with the Manure} -Once all the animal chores are finished, Dr. Rue moves on to handling the manure. There are a lot of different ways that manure is collected from the animals: it is flushed out of the milking parlor with water, some of the pens need to have it shoveled out along with the bedding in the pen, and some pens have grates that allow the manure to go straight into a pit beneath the barn. -\vspace{0.2cm} - -There are a lot of different places where manure is processed and stored on the farm. Dr. Rue goes from place to place on the farm, moving the manure from one place to the next. The manure chores are finished after moving all of the manure into her lagoons, compost piles, and other storages. As this final manure chore is completed, she writes down all the information about how much manure is in all these storages, and some information about what that manure is made of. How much water, nitrogen, phosphorus, other solids, etc. are in each storage. - -\paragraph{Managing the Fields} -Now that Dr. Rue is done making sure all the manure has been handled and stored properly, she can take care of all the field tasks. She has a lot of fields on her farm, each with its own unique schedule. Her field management routine starts with checking each field’s schedule to see if any of them are due to have manure applied, and if so, how much they should have applied. After noting all the manure that is supposed to go onto her fields, these amounts are checked against the amounts of manure that are in her manure storage. Dr. Rue then applies manure to each field on the schedule that day, trying to match the amount applied to the amount on the schedule as best she can. -\vspace{0.2cm} - -After making sure every manure item on each farm’s schedule has been taken care of for the day, the schedule for each field is rechecked, one field at a time. In each schedule she checks to see if that field needs to be tilled, if any chemical fertilizer needs to be applied, and if any crops need to be planted or harvested. After all these activities are taken care of, Mother Nature goes to work. The sun shines and rain falls, providing the field with water and energy that grows crops and soaks the soil. After taking care of each field one by one, Dr. Rue drives back to the main farm with all of the crops that she harvested on that day. - -\paragraph{Storing the Feeds} -Now that she is back at the barns, all the crops that were just harvested can be stored. Fortunately she is very organized, so all her harvested crops are separate from one another and each has a label, indicating where it will be stored inside the feed barn. As each feed is stored, it is labeled with the current date. Dr. Rue is exhausted from another long day. She goes back to the farmhouse and rests up, preparing to do the whole thing over again tomorrow. Her daily routine might seem repetitive, but each day is a crucial part of the larger, continuous process that keeps her farm running efficiently and sustainably. - - +\section*{List of Tables} +\locallistoftables \newpage - \section{Module Introduction} +\par\noindent\justifying + The Soil and Crop Module simulates the daily changes in soil composition and crop growth based on nutrient availability, weather and soil types. The underlying biophysical processes are drawn from existing models of soil and plant biogeochemistry including the SWAT model, Daycent, and SurPhos. The management routines execute the daily biogeochemical processes and direct simulation of the user-provided management practices including application of manure or synthetic fertilizer, tillage, planting and harvesting. As part of the whole farm biophysical simulation in RuFaS, the Soil and Crop Module receives manure from the Manure Module and sends harvested crop biomass to the Feed Storage Module. \vspace{0.2cm} + \section{Field Management} \subsection{Introduction} The Field Manager (FieldManager) is analogous to the agronomist or field manager on a real dairy farm. It coordinates and manages all the different routines and processes that are executed in Soil and Crop Module across any number of fields. To start with, the field manager interprets and integrates all of the user’s inputs about field management, crops, and soils to create a set of fields that each have their specified field and soil properties as well as schedules for each of the key management operations (manure application, fertilizer application, tillage, planting, and harvesting). @@ -301,7 +74,7 @@ \subsection{Introduction} \centering \includegraphics[width=0.9\textwidth]{resources/metadatainput.png} % Replace with your image file \caption{Example of the metadata input file.} - \label{fig:example} + \end{figure} @@ -941,7 +714,7 @@ \subsection{Methodology} -\section{Soil Management} \label{soilmgt} +\section{Soil Management} \subsection{Introduction} \vspace{0.2cm} @@ -4466,7 +4239,7 @@ \subsection{Methodology} \paragraph{Crop Evaporation} \vspace{-0.25cm} -The maximum potential crop canopy evaporation and transpiration are calculated as a function of the total potential evapotranspiration for the field on that day (see the \hyperref[soilmgt]{Soil documentation}). +The maximum potential crop canopy evaporation and transpiration are calculated as a function of the total potential evapotranspiration for the field on that day (see the Soil documentation). After the total potential evapotranspiration (mm H\textsubscript{2}O) is calculated in the Field class, evaporation from the crop canopy is estimated as: @@ -5705,105 +5478,6 @@ \subsection{Methodology} This method relies on two crop-specific, empirically fitted parameters estimated by \cite{fan2016root}: root\_dist\_param\_c and root\_dist\_param\_c. The default values for these parameters are those reported in the original manuscript but they are available for adjustment as user inputs. -\newpage -\section{Abbreviations} - -\renewcommand{\arraystretch}{1.3} -\newcolumntype{L}[1]{>{\RaggedRight\arraybackslash}p{#1}} - -% optionally tighten column padding just for this table -\setlength{\tabcolsep}{4pt} - -\begin{longtable}{@{} L{0.23\textwidth} L{0.70\textwidth} @{}} % 0.93*textwidth + padding < textwidth -\caption{Common abbreviations used throughout this document} \\ - -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endfirsthead - -\multicolumn{2}{@{}l}{\textit{Table continued from previous page}} \\ -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endhead - -\midrule -\multicolumn{2}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot - -\bottomrule -\endlastfoot - -ADF & Acid detergent fiber (\% of DM) \\ -ADG & Average daily weight gain (g/d) \\ -Age1stBred & First breeding age (month) \\ -BCS5 & Body condition score (1–5 basis) \\ -BW & Body weight (kg) \\ -Ca & Calcium content (\% of DM) \\ -CBW & Calf birth weight (kg) \\ -CI & Calving interval (d) \\ -cm & centimeter \\ -Cost & Feed cost (\$/kg of DM) \\ -CP & Crude protein (\% of DM) \\ -d & days \\ -DE & Digestible energy (standard value, Mcal/kg) \\ -DIM & Days in milk \\ -DM & Dry matter (\% of as-fed basis) \\ -DMI & Dry matter intake \\ -DOP & Days of pregnancy (d) \\ -dRUP & RUP degradability (\% of RUP) \\ -EE & Ether extract, in crude fat (\% DM) \\ -EndCP & Endogenous CP \\ -EndN & Endogenous N \\ -EQSBW & Equivalent shrunk body weight (kg) \\ -FA & Fatty acids \\ -FIPS & Federal Information Processing Standards \\ -g & grams \\ -GE & Gross energy (standard value, Mcal/kg) \\ -GrUterW & Gravid uterine weight (kg) \\ -Kd & Rumen protein degradation rate (\%/h) \\ -kg & kilograms \\ -kJ & kilojoule \\ -L & liters \\ -m & meter \\ -max & maximum \\ -Mcal & Megacalorie \\ -MCP & Microbial Crude Protein \\ -ME & Metabolizable energy (standard value, Mcal/kg) \\ -MICP & Microbial CP \\ -min & minimum \\ -mL & milliliters \\ -MN & Microbial N \\ -MP & Metabolizable protein \\ -MTP & Microbial TP \\ -MW & Mature body weight (kg) \\ -MY & Milk yield \\ -N & Nitrogen (\% of DM) \\ -NASEM & National Academies of Sciences, Engineering, and Medicine \\ -NDF & Neutral detergent fiber (\% of DM) \\ -NEG & Net energy for growth (standard value, Mcal/kg) \\ -NEL & Net energy for lactation (standard value, Mcal/kg) \\ -NEM & Net energy for maintenance (standard value, Mcal/kg) \\ -nNDF & Nondigestible Neutral Detergent Fiber \\ -NPN & Non-protein Nitrogen \\ -NRC & National Research Council (updated in 2021 to NASEM) \\ -OM & Organic matter (\% of DM) \\ -P & Phosphorus content (\% of DM) \\ -PAF & Processing adjustment factor (not used) \\ -Parity & Number of lactations \\ -PrevTemp & Average daily temperature of last month (°C) \\ -RDP & Ruminally degraded CP \\ -ROM & Residual OM (\% of DM) \\ -RUP & Ruminally undegraded CP \\ -s & seconds \\ -TAN & Total ammoniacal N \\ -TDN & Total digestible nutrient (\% of DM) \\ -TP & True protein (\% of DM) \\ -USDA & United States Department of Agriculture \\ -UterW & Uterine weight (kg) \\ -WSC & Water Soluble Carbohydrates \\ -\end{longtable} @@ -5813,4 +5487,3 @@ \section{Abbreviations} \printbibliography[heading=subbibliography,title={References for Crop and Soil Module}] \end{refsection} -\end{document} \ No newline at end of file diff --git a/docs/scientific/cropandsoilmoddoc.aux b/docs/scientific/cropandsoilmoddoc.aux new file mode 100644 index 0000000000..99d20cc28b --- /dev/null +++ b/docs/scientific/cropandsoilmoddoc.aux @@ -0,0 +1,77 @@ +\relax +\providecommand\babel@aux[2]{} +\@nameuse{bbl@beforestart} +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\catcode 95\active 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authoryear.bbx + authoryear.cbx + biblatex.cfg + english.lbx + + + + biber + + biber + cropandsoilmoddoc + + + cropandsoilmoddoc.bcf + + + cropandsoilmoddoc.bbl + + + cropandsoilmoddoc.bbl + + + cropandsoilmoddoc.bcf + + + resources/animal.bib + + + diff --git a/docs/scientific/cropandsoilmoddoc.synctex.gz b/docs/scientific/cropandsoilmoddoc.synctex.gz new file mode 100644 index 0000000000..264b44384d Binary files /dev/null and b/docs/scientific/cropandsoilmoddoc.synctex.gz differ diff --git a/docs/scientific/cropandsoilmoddoc.tex b/docs/scientific/cropandsoilmoddoc.tex new file mode 100644 index 0000000000..30bf52ce8d --- /dev/null +++ b/docs/scientific/cropandsoilmoddoc.tex @@ -0,0 +1,33 @@ +\documentclass{article} + +\input{preamble} + +\begin{document} + + + \thispagestyle{empty} + \centering + \vspace*{2cm} + + {\Huge\bfseries Crop and Soil Module\par} + \vspace{1cm} + + {\Large RuFaS Scientific Documentation\par} + \vspace{1cm} + + \includegraphics[width=0.5\textwidth]{resources/crop.png} % Adjust size and filename + + \vfill + + {\small v.1\par} + \vspace*{1cm} + +\newpage + + +% Continue with front matter (e.g., table of contents) +\thispagestyle{fancy} % Ensure the header/footer appears on the first page + +\include{crop_and_soil} + +\end{document} \ No newline at end of file diff --git a/docs/scientific/cropandsoilmoddoc.toc b/docs/scientific/cropandsoilmoddoc.toc new file mode 100644 index 0000000000..33916ec51a --- /dev/null +++ b/docs/scientific/cropandsoilmoddoc.toc @@ -0,0 +1,85 @@ +\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{} +\babel@toc {english}{}\relax +\contentsline {part}{I\hspace {1em}Soil and Crop Module}{2}{part.1}% +\etoc@startlocaltoc {1} +\contentsline {section}{\numberline {I.}Module Introduction}{5}{section.1}% +\contentsline {section}{\numberline {II.}Field Management}{5}{section.2}% +\contentsline {subsection}{\numberline {A.}Introduction}{5}{subsection.2.1}% +\contentsline {paragraph}{Setting up Field Management}{5}{subsection.2.1}% +\contentsline {paragraph}{Field Management Initialization}{5}{subsection.2.1}% +\contentsline {paragraph}{Field Setup and Initialization}{6}{figure.caption.1}% +\contentsline {paragraph}{Required Inputs}{7}{figure.caption.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{13}{subsection.2.2}% +\contentsline {paragraph}{Daily Field Management}{14}{subsection.2.2}% +\contentsline {paragraph}{Fertilizer Application}{15}{subsection.2.2}% +\contentsline {paragraph}{Where:}{15}{subsection.2.2}% +\contentsline {paragraph}{Where:}{15}{subsection.2.2}% +\contentsline {paragraph}{Where:}{16}{subsection.2.2}% +\contentsline {paragraph}{Where:}{17}{subsection.2.2}% +\contentsline {paragraph}{Manure Application}{17}{subsection.2.2}% +\contentsline {paragraph}{Where:}{18}{subsection.2.2}% +\contentsline {paragraph}{Surface Manure Application}{18}{subsection.2.2}% +\contentsline {paragraph}{Where:}{18}{subsection.2.2}% +\contentsline {paragraph}{Surface Phosphorus Application}{18}{subsection.2.2}% +\contentsline {paragraph}{Where:}{19}{subsection.2.2}% +\contentsline {paragraph}{Surface Nitrogen Application}{19}{subsection.2.2}% +\contentsline {paragraph}{Where:}{20}{subsection.2.2}% +\contentsline {paragraph}{Subsurface Manure Application}{20}{subsection.2.2}% +\contentsline {paragraph}{Tillage Application}{21}{subsection.2.2}% +\contentsline {paragraph}{Initiate Daily Biophysical Processes}{21}{subsection.2.2}% +\contentsline {paragraph}{Crop Management}{21}{subsection.2.2}% +\contentsline {section}{\numberline {III.}Soil Management}{21}{section.3}% +\contentsline {subsection}{\numberline {A.}Introduction}{21}{subsection.3.1}% +\contentsline {paragraph}{Soil Initialization}{22}{subsection.3.1}% +\contentsline {paragraph}{Required Inputs}{23}{subsection.3.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{26}{subsection.3.2}% +\contentsline {paragraph}{Soil Temperature}{26}{subsection.3.2}% +\contentsline {paragraph}{Infiltration (implemented in infiltration.py)}{28}{subsection.3.2}% +\contentsline {paragraph}{Evapotranspiration}{30}{subsection.3.2}% +\contentsline {paragraph}{Potential Evapotranspiration (Implemented in field.py)}{31}{subsection.3.2}% +\contentsline {paragraph}{Percolation (implemented in percolation.py)}{33}{subsection.3.2}% +\contentsline {subsection}{\numberline {C.}Soil Erosion (Implemented as soil\_erosion.py)}{34}{subsection.3.3}% +\contentsline {paragraph}{Base Equation, Rainfall Intensity, and Peak Runoff}{34}{subsection.3.3}% +\contentsline {subsection}{\numberline {D.}Soil Nitrogen Cycling}{38}{subsection.3.4}% +\contentsline {paragraph}{Nitrification and Volatilization (Implemented in nitirification\_volatilization.py)}{40}{subsection.3.4}% +\contentsline {paragraph}{N loss in leaching and runoff (Implemented in leaching\_runoff\_erosion.py)}{42}{subsection.3.4}% +\contentsline {paragraph}{N erosion (Implemented in leaching\_runoff\_erosion.py)}{43}{subsection.3.4}% +\contentsline {paragraph}{Denitrification (Implemented in denitrification.py)}{44}{subsection.3.4}% +\contentsline {subsection}{\numberline {E.}Soil Phosphorus Cycling}{48}{subsection.3.5}% +\contentsline {paragraph}{Phosphorus Initialization (Implemented in layer\_data.py)}{48}{subsection.3.5}% +\contentsline {paragraph}{Soluble Phosphorus (Implemented in soluble\_phosphorus.py)}{49}{subsection.3.5}% +\contentsline {paragraph}{Soluble Phosphorus Runoff}{49}{subsection.3.5}% +\contentsline {paragraph}{Soluble Phosphorus Leaching}{50}{subsection.3.5}% +\contentsline {paragraph}{Fertilizer Leaching and Runoff (Implemented in fertilizer.py)}{51}{subsection.3.5}% +\contentsline {paragraph}{Available Fertilizer P pool }{51}{subsection.3.5}% +\contentsline {paragraph}{Manure Decomposition (implemented in manure\_pool.py)}{55}{subsection.3.5}% +\contentsline {paragraph}{Manure Runoff (implemented in manure\_pool.py)}{58}{subsection.3.5}% +\contentsline {subsection}{\numberline {F.}Soil Carbon Cycling}{61}{subsection.3.6}% +\contentsline {paragraph}{Soil Carbon Partitioning (implemented in carbon\_cycle.py)}{61}{subsection.3.6}% +\contentsline {paragraph}{Decomposition (implemented in decomposition.py)}{62}{subsection.3.6}% +\contentsline {paragraph}{Residue Partitioning (implemented in residue\_partitioning.py)}{65}{subsection.3.6}% +\contentsline {paragraph}{Above Ground: Lignin, Metabolic C, Structural C}{66}{subsection.3.6}% +\contentsline {paragraph}{Pool and Gas Partitioning (implemented in pool\_gas\_partition.py)}{70}{subsection.3.6}% +\contentsline {section}{\numberline {IV.}Crop Management}{74}{section.4}% +\contentsline {subsection}{\numberline {A.}Introduction}{74}{subsection.4.1}% +\contentsline {paragraph}{Planting and Initialization}{75}{subsection.4.1}% +\contentsline 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-\renewcommand{\thesection}{\Roman{section}.} % I, II, III... -\renewcommand{\thesubsection}{\Alph{subsection}.} % A, B, C... -\renewcommand{\thesubsubsection}{\alph{subsubsection}.} % a, b, c... - -% --- Title Formats (in size order) --- -\titleformat{\section} - {\Large\bfseries} % Section: largest - {\thesection} % Label - {1em} % Spacing between label and title - {} % Before-code - -\titleformat{\subsection} - {\normalsize\bfseries} % Subsection: medium - {\thesubsection} - {1em} - {} - -\titleformat{\subsubsection} - {\normalsize\bfseries} % Subsubsection: smallest - {\thesubsubsection} - {1em} - {} - -% --- Spacing for each level --- -\titlespacing{\section}{0pt}{10pt plus 2pt minus 1pt}{5pt} -\titlespacing{\subsection}{0pt}{8pt plus 1pt minus 1pt}{4pt} -\titlespacing{\subsubsection}{0pt}{6pt plus 1pt minus 1pt}{3pt} - -% Optional: Keep your TOC control if needed -\usepackage{etoc} - -% Optional: If using headers/footers -\renewcommand{\sectionmark}[1]{\markboth{#1}{}} - -% Remove default date from title -\date{} % Prevents date from appearing in \maketitle - - -% Define title -\title{\textbf{}} -\author{ } -\setlength{\topskip}{10pt} % Ensures LaTeX reserves room above the first line -%\usepackage{showframe} - -\begin{document} - -% Custom Title Page -\begin{titlepage} - \thispagestyle{empty} - \centering - \vspace*{2cm} - - {\Huge\bfseries Ruminant Farm System Model\par} - \vspace{1cm} - - {\Large Feed Storage Module\par} - \vspace{1cm} - - {\large \today\par} - \vspace{1.5cm} % Add space before the image - - \includegraphics[width=0.25\textwidth]{resources/feed.png} % Adjust size and filename - - \vfill - - {\small v.1; Updated 2026\par} - \vspace*{1cm} -\end{titlepage} - -% Continue with front matter (e.g., table of contents) -\thispagestyle{fancy} % Ensure the header/footer appears on the first page - +\part{Feed Storage Module} % Global Table of Contents \thispagestyle{fancy} -\tableofcontents -\newpage -\listoffigures -\newpage +% Local TOC that includes only what’s inside THIS section +\etocsettocstyle{\subsection*{Contents}}{} % heading for the local toc +\etocsetnexttocdepth{subsection} % or subsubsection +\localtableofcontents +\clearpage -\listoftables +\section*{List of Figures} +\locallistoffigures \newpage -\newpage -\section{Preface: A Day in the Life on a RuFaS Farm} - -This document provides a high-level overview of the daily operations of a ruminant farm, as modeled by RuFaS. The overview will be through the eyes of Dr. Rue Fas. One day, Dr. Rue woke up and decided the life of a computer scientist wasn’t for her. So she bought a dairy farm, and this is how she operates it every day. - -\paragraph{Feeding the Animals} -Second thing in the morning, after coffee, Dr. Rue checks the calendar to see if it’s time to formulate a new ration for her animals. -\vspace{0.2cm} - -If a new ration needs to be formulated, Dr. Rue heads over to the barn where she keeps all her forages and feed. While there, she checks how well all the forages are holding up. After considering the feeds available, the quality of each one, and how much each one costs, she decides on how productive she wants her animals to be. It is a difficult balancing act, but eventually a ration recipe is found that will keep the animals happy while keeping costs low and sustainability high until the calendar says the ration recipe needs to be reformulated. -\vspace{0.2cm} - -When Dr. Rue doesn’t need to formulate a new ration, she takes the last ration recipe she made and grabs all the feed and forage the animals need for the day out of the feed barn. If there isn’t enough for the animals, then a new ration is formulated using the steps above. - -\paragraph{Taking Care of the Animals} -After making sure all the animals’ feed is taken care of, Dr. Rue moves on to taking care of all the other animal tasks. This includes milking the animals, making sure they’re healthy, getting them pregnant, and numerous other tasks. -\vspace{0.2cm} - -As dawn breaks on the RuFaS farm, the animals awaken after a restful night. Joe, the farm master, prepares a large whiteboard to track HerdReproductionStatistics, ensuring he has all the data he needs for the day’s activities. - -\textit{Daily Routine} - After leaving their pens, each animal lines up in front of the barn. Julie, the diligent farm veterinarian, examines them one by one. This daily check includes updates on the following areas: -\begin{itemize} - \item Nutrients: Each animal begins its day with a quick phosphorus requirement assessment. Julie records these details and updates the animal’s phosphorus-related metrics. - \item Digestive System: With nutrient information in hand, Julie shifts focus to each animal’s digestive system, estimating manure output and enteric methane production for that day. - - \item Milk Production: All milking cows are assessed to gauge daily milk yield and milk component content (fat and protein). Any necessary adjustments are noted. - - \item Animal Growth: Around midday, Julie returns to each animal to evaluate daily weight changes. She updates each animal’s body weight accordingly. - - \item Reproduction: HeiferII and Cow stage animals undergo a reproduction check. Julie closely monitors their reproductive progress and updates the HerdReproductionStatistics details on Joe’s whiteboard. - - \item Life Stage Evaluation: Once the daily routines are complete, Julie determines if any animal is ready to progress to the next life stage. Graduating animals are marked as “graduated” to be moved to their new pens. Animals that must leave the herd—due to health, productivity, or other issues—are labeled as “sold” or “dead” to be removed from the farm population. - - \item Herd Size Maintenance: After every animal has been evaluated, Joe counts the herd to ensure it remains at a healthy size. If it is too large, he arranges the sale of some animals. If the herd is too small, he may opt to purchase additional heiferIIIs to keep numbers at the ideal level. - - \item Herd Structure Management: Joe also manages pen assignments. Newly graduated or newborn animals are guided to suitable pens, while animals marked for removal (sold or deceased) are taken out of the herd and removed from the farm records. -\end{itemize} - - -\textit{Output Reporting} -At day’s end, Joe and Julie review the updated HerdReproductionStatistics on the whiteboard. Joe then compiles a concise report summarizing the day’s herd stats. He forwards this information to the OutputManager before wrapping up another successful day on the RuFaS farm. -\vspace{0.5cm} - -\paragraph{Dealing with the Manure} -Once all the animal chores are finished, Dr. Rue moves on to handling the manure. There are a lot of different ways that manure is collected from the animals: it is flushed out of the milking parlor with water, some of the pens need to have it shoveled out along with the bedding in the pen, and some pens have grates that allow the manure to go straight into a pit beneath the barn. -\vspace{0.2cm} - -There are a lot of different places where manure is processed and stored on the farm. Dr. Rue goes from place to place on the farm, moving the manure from one place to the next. The manure chores are finished after moving all of the manure into her lagoons, compost piles, and other storages. As this final manure chore is completed, she writes down all the information about how much manure is in all these storages, and some information about what that manure is made of. How much water, nitrogen, phosphorus, other solids, etc. are in each storage. - -\paragraph{Managing the Fields} -Now that Dr. Rue is done making sure all the manure has been handled and stored properly, she can take care of all the field tasks. She has a lot of fields on her farm, each with its own unique schedule. Her field management routine starts with checking each field’s schedule to see if any of them are due to have manure applied, and if so, how much they should have applied. After noting all the manure that is supposed to go onto her fields, these amounts are checked against the amounts of manure that are in her manure storage. Dr. Rue then applies manure to each field on the schedule that day, trying to match the amount applied to the amount on the schedule as best she can. -\vspace{0.2cm} - -After making sure every manure item on each farm’s schedule has been taken care of for the day, the schedule for each field is rechecked, one field at a time. In each schedule she checks to see if that field needs to be tilled, if any chemical fertilizer needs to be applied, and if any crops need to be planted or harvested. After all these activities are taken care of, Mother Nature goes to work. The sun shines and rain falls, providing the field with water and energy that grows crops and soaks the soil. After taking care of each field one by one, Dr. Rue drives back to the main farm with all of the crops that she harvested on that day. - -\paragraph{Storing the Feeds} -Now that she is back at the barns, all the crops that were just harvested can be stored. Fortunately she is very organized, so all her harvested crops are separate from one another and each has a label, indicating where it will be stored inside the feed barn. As each feed is stored, it is labeled with the current date. Dr. Rue is exhausted from another long day. She goes back to the farmhouse and rests up, preparing to do the whole thing over again tomorrow. Her daily routine might seem repetitive, but each day is a crucial part of the larger, continuous process that keeps her farm running efficiently and sustainably. +\section*{List of Tables} +\locallistoftables \newpage \section{Module Introduction} \begin{refsection} -The Feed Module’s primary purpose is to serve as an inventory of purchased and farm-grown feed. Feed is added via purchase (Animal Module) and from on-farm harvest (Crop and Soil Module). Feed is removed when it is fed out in the Animal Module. In addition, stored feed quantity and quality changes are simulated over the duration of storage depending on crop type, crop quality, user-specified storage conditions, and ambient climate conditions. The feed storage module currently accepts Corn (silage, dry/high-moisture grain), Alfalfa, Grass, Triticale/Cereal, and Soybean. Forage and/or feed quality can also be user-specified, offering flexibility and modularity of user needs. Feed component values, proportions, digestibility, and availability subject to change during storage are: mass, DM content, CP, NPN, nNDF, ADF, starch, and WSC. These changes must be tracked to accurately reflect the remaining feed and its qualities. Overall stored feed quality is \hyperref[feedqualassess]{assessed} prior to consumption in the \hyperref[animalmodule]{Animal Module}. + \par\noindent\justifying + +The Feed Module’s primary purpose is to serve as an inventory of purchased and farm-grown feed. Feed is added via purchase (Animal Module) and from on-farm harvest (Crop and Soil Module). Feed is removed when it is fed out in the Animal Module. In addition, stored feed quantity and quality changes are simulated over the duration of storage depending on crop type, crop quality, user-specified storage conditions, and ambient climate conditions. The feed storage module currently accepts Corn (silage, dry/high-moisture grain), Alfalfa, Grass, Triticale/Cereal, and Soybean. Forage and/or feed quality can also be user-specified, offering flexibility and modularity of user needs. Feed component values, proportions, digestibility, and availability subject to change during storage are: mass, DM content, CP, NPN, nNDF, ADF, starch, and WSC. These changes must be tracked to accurately reflect the remaining feed and its qualities. Overall stored feed quality is assessed prior to consumption in the Animal Module. -\subsection{Feed Quality Assessment} \label{feedqualassess} +\subsection{Feed Quality Assessment} colorbox This section allocates farm grown feeds to be used for single or multiple animal classes and is illustrated in Figure 1. Priority is to reserve high-quality forage for lactating cows. Feeds are generally categorized into grains or forages. If the feed is a grain then it is available to all animal classes. The model assumes that grains can be purchased to supplement farm grown grain inventory. If the feed is a forage, then some farms will assess the quality of the forage and preserve the high quality forage for the lactating cows. If they do not differentiate their forages based on quality, then the forage is available to all animals. @@ -251,7 +32,6 @@ \subsection{Feed Quality Assessment} \label{feedqualassess} \centering \includegraphics[width=0.9\textwidth]{resources/feedallocation.png} % Replace with your image file \caption{Farm grown feed allocation to cattle groups } - \label{fig:example} \end{figure} @@ -635,108 +415,9 @@ \subsection{Nutrient Composition} -\newpage -\section{Abbreviations} - -\renewcommand{\arraystretch}{1.3} -\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}} - -\begin{longtable}{@{} L{4cm} L{12cm} @{}} -\caption{Common abbreviations used throughout this document} \\ - -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endfirsthead - -\multicolumn{2}{@{}l}{\textit{Table continued from previous page}} \\ -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endhead - -\midrule -\multicolumn{2}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot - -\bottomrule -\endlastfoot - -ADF & Acid detergent fiber (\% of DM) \\ -ADG & Average daily weight gain (g/d) \\ -Age1stBred & First breeding age (month) \\ -BCS5 & Body condition score (1–5 basis) \\ -BW & Body weight (kg) \\ -Ca & Calcium content (\% of DM) \\ -CBW & Calf birth weight (kg) \\ -CI & Calving interval (d) \\ -cm & centimeter \\ -Cost & Feed cost (\$/kg of DM) \\ -CP & Crude protein (\% of DM) \\ -d & days \\ -DE & Digestible energy (standard value, Mcal/kg) \\ -DIM & Days in milk \\ -DM & Dry matter (\% of as-fed basis) \\ -DMI & Dry matter intake \\ -DOP & Days of pregnancy (d) \\ -dRUP & RUP degradability (\% of RUP) \\ -EE & Ether extract, in crude fat (\% DM) \\ -EndCP & Endogenous CP \\ -EndN & Endogenous N \\ -EQSBW & Equivalent shrunk body weight (kg) \\ -FA & Fatty acids \\ -FIPS & Federal Information Processing Standards \\ -g & grams \\ -GE & Gross energy (standard value, Mcal/kg) \\ -GrUterW & Gravid uterine weight (kg) \\ -Kd & Rumen protein degradation rate (\%/h) \\ -kg & kilograms \\ -kJ & kilojoule \\ -L & liters \\ -m & meter \\ -max & maximum \\ -Mcal & Megacalorie \\ -MCP & Microbial Crude Protein \\ -ME & Metabolizable energy (standard value, Mcal/kg) \\ -MICP & Microbial CP \\ -min & minimum \\ -mL & milliliters \\ -MN & Microbial N \\ -MP & Metabolizable protein \\ -MTP & Microbial TP \\ -MW & Mature body weight (kg) \\ -MY & Milk yield \\ -N & Nitrogen (\% of DM) \\ -NASEM & National Academies of Sciences, Engineering, and Medicine \\ -NDF & Neutral detergent fiber (\% of DM) \\ -NEG & Net energy for growth (standard value, Mcal/kg) \\ -NEL & Net energy for lactation (standard value, Mcal/kg) \\ -NEM & Net energy for maintenance (standard value, Mcal/kg) \\ -nNDF & Nondigestible Neutral Detergent Fiber \\ -NPN & Non-protein Nitrogen \\ -NRC & National Research Council (updated in 2021 to NASEM) \\ -OM & Organic matter (\% of DM) \\ -P & Phosphorus content (\% of DM) \\ -PAF & Processing adjustment factor (not used) \\ -Parity & Number of lactations \\ -PrevTemp & Average daily temperature of last month (°C) \\ -RDP & Ruminally degraded CP \\ -ROM & Residual OM (\% of DM) \\ -RUP & Ruminally undegraded CP \\ -s & seconds \\ -TAN & Total ammoniacal N \\ -TDN & Total digestible nutrient (\% of DM) \\ -TP & True protein (\% of DM) \\ -USDA & United States Department of Agriculture \\ -UterW & Uterine weight (kg) \\ -WSC & Water Soluble Carbohydrates \\ -\end{longtable} \newpage \section{References} \printbibliography[heading=subbibliography,title={Feed Storage Module}] -\end{refsection} - - -\end{document} +\end{refsection} \ No newline at end of file diff --git a/docs/scientific/feedstoragemoddoc.aux b/docs/scientific/feedstoragemoddoc.aux new file mode 100644 index 0000000000..43973c2726 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.aux @@ -0,0 +1,27 @@ +\relax +\providecommand\babel@aux[2]{} +\@nameuse{bbl@beforestart} +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\catcode 95\active +\abx@aux@refcontext{nyt/global//global/global} +\@writefile{toc}{\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{}} +\babel@aux{english}{} +\@input{feed_storage.aux} +\abx@aux@refsection{1}{5} +\abx@aux@cite{1}{pahlow2003microbiology} +\abx@aux@segm{1}{0}{pahlow2003microbiology} +\abx@aux@cite{1}{pahlow2003microbiology} +\abx@aux@segm{1}{0}{pahlow2003microbiology} +\abx@aux@cite{1}{muck2013recent} +\abx@aux@segm{1}{0}{muck2013recent} +\abx@aux@page{1}{9} +\abx@aux@page{2}{9} +\abx@aux@page{3}{9} +\abx@aux@page{4}{13} +\abx@aux@page{5}{13} +\abx@aux@read@bbl@mdfivesum{3677A27EA070380EA49B09BF51663547} +\abx@aux@defaultrefcontext{1}{muck2013recent}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{pahlow2003microbiology}{nyt/global//global/global} +\gdef \@abspage@last{13} diff --git a/docs/scientific/feedstoragemoddoc.bbl b/docs/scientific/feedstoragemoddoc.bbl new file mode 100644 index 0000000000..361102eef8 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.bbl @@ -0,0 +1,134 @@ +% $ biblatex auxiliary file $ +% $ biblatex bbl format version 3.2 $ +% Do not modify the above lines! +% +% This is an auxiliary file used by the 'biblatex' package. +% This file may safely be deleted. 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Config.pm:307> INFO - This is Biber 2.19 +[0] Config.pm:310> INFO - Logfile is 'feedstoragemoddoc.blg' +[216] biber-MSWIN64:340> INFO - === +[275] Biber.pm:419> INFO - Reading 'feedstoragemoddoc.bcf' +[444] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[444] Biber.pm:979> INFO - Found 2 citekeys in bib section 1 +[444] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[494] Biber.pm:4419> INFO - Processing section 1 +[526] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1 +[603] bibtex.pm:1713> INFO - LaTeX decoding ... +[765] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib' +[909] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[909] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[909] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[909] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[914] bbl.pm:660> INFO - Writing 'feedstoragemoddoc.bbl' with encoding 'UTF-8' +[921] bbl.pm:763> INFO - Output to feedstoragemoddoc.bbl diff --git a/docs/scientific/feedstoragemoddoc.fdb_latexmk b/docs/scientific/feedstoragemoddoc.fdb_latexmk new file mode 100644 index 0000000000..3652c4be55 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.fdb_latexmk @@ -0,0 +1,270 @@ +# Fdb version 4 +["biber feedstoragemoddoc"] 1772715847.05047 "feedstoragemoddoc.bcf" "feedstoragemoddoc.bbl" "feedstoragemoddoc" 1772723128.47318 0 + "feedstoragemoddoc.bcf" 1772723127 108268 50df1d17e77d41a523be630ec1d9fb94 "pdflatex" + "resources/animal.bib" 1772218264 19843 003ce6dc3163a9c1fd885dbc082d404e "" + (generated) + "feedstoragemoddoc.bbl" + "feedstoragemoddoc.blg" + (rewritten before read) +["pdflatex"] 1772723125.19384 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/feedstoragemoddoc.tex" 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b/docs/scientific/feedstoragemoddoc.lof new file mode 100644 index 0000000000..b4ac22b075 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.lof @@ -0,0 +1,2 @@ +\babel@toc {english}{}\relax +\contentsline {figure}{\numberline {1}{\ignorespaces Farm grown feed allocation to cattle groups }}{5}{figure.caption.1}% diff --git a/docs/scientific/feedstoragemoddoc.lot b/docs/scientific/feedstoragemoddoc.lot new file mode 100644 index 0000000000..fe33caa952 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.lot @@ -0,0 +1,4 @@ +\babel@toc {english}{}\relax +\contentsline {table}{\numberline {1}{\ignorespaces Hay storage types and associated fractional loss coefficients}}{8}{table.caption.2}% +\contentsline {table}{\numberline {2}{\ignorespaces Protected and unprotected storage, nutrients, and associated fractional loss coefficients}}{9}{table.caption.3}% +\contentsline {table}{\numberline {3}{\ignorespaces Silage and the fractional loss coefficients}}{10}{table.caption.4}% diff --git a/docs/scientific/feedstoragemoddoc.out b/docs/scientific/feedstoragemoddoc.out new file mode 100644 index 0000000000..dd6a107a89 --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.out @@ -0,0 +1,11 @@ +\BOOKMARK [0][-]{part.1}{\376\377\000I\000\040\000F\000e\000e\000d\000\040\000S\000t\000o\000r\000a\000g\000e\000\040\000M\000o\000d\000u\000l\000e}{}% 1 +\BOOKMARK [1][-]{section.1}{\376\377\000M\000o\000d\000u\000l\000e\000\040\000I\000n\000t\000r\000o\000d\000u\000c\000t\000i\000o\000n}{part.1}% 2 +\BOOKMARK [2][-]{subsection.1.1}{\376\377\000F\000e\000e\000d\000\040\000Q\000u\000a\000l\000i\000t\000y\000\040\000A\000s\000s\000e\000s\000s\000m\000e\000n\000t}{section.1}% 3 +\BOOKMARK [1][-]{section.2}{\376\377\000F\000e\000e\000d\000\040\000S\000t\000o\000r\000a\000g\000e\000\040\000I\000n\000p\000u\000t\000s}{part.1}% 4 +\BOOKMARK 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a/docs/scientific/feedstoragemoddoc.run.xml b/docs/scientific/feedstoragemoddoc.run.xml new file mode 100644 index 0000000000..a1146b3cea --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.run.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + +]> + + + latex + + feedstoragemoddoc.bcf + + + feedstoragemoddoc.bbl + + + blx-dm.def + blx-compat.def + biblatex.def + blx-natbib.def + standard.bbx + authoryear.bbx + authoryear.cbx + biblatex.cfg + english.lbx + + + + biber + + biber + feedstoragemoddoc + + + feedstoragemoddoc.bcf + + + feedstoragemoddoc.bbl + + + feedstoragemoddoc.bbl + + + feedstoragemoddoc.bcf + + + resources/animal.bib + + + diff --git a/docs/scientific/feedstoragemoddoc.synctex.gz b/docs/scientific/feedstoragemoddoc.synctex.gz new file mode 100644 index 0000000000..105a3f8992 Binary files /dev/null and b/docs/scientific/feedstoragemoddoc.synctex.gz differ diff --git a/docs/scientific/feedstoragemoddoc.tex b/docs/scientific/feedstoragemoddoc.tex new file mode 100644 index 0000000000..8988328b5a --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.tex @@ -0,0 +1,33 @@ +\documentclass{article} + +\input{preamble} + +\begin{document} + + + \thispagestyle{empty} + \centering + \vspace*{2cm} + + {\Huge\bfseries Feed Storage Module\par} + \vspace{1cm} + + {\Large RuFaS Scientific Documentation\par} + \vspace{1cm} + + \includegraphics[width=0.5\textwidth]{resources/feed.png} % Adjust size and filename + + \vfill + + {\small v.1\par} + \vspace*{1cm} + +\newpage + + +% Continue with front matter (e.g., table of contents) +\thispagestyle{fancy} % Ensure the header/footer appears on the first page + +\include{feed_storage} + +\end{document} \ No newline at end of file diff --git a/docs/scientific/feedstoragemoddoc.toc b/docs/scientific/feedstoragemoddoc.toc new file mode 100644 index 0000000000..aa101810eb --- /dev/null +++ b/docs/scientific/feedstoragemoddoc.toc @@ -0,0 +1,14 @@ +\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{} +\babel@toc {english}{}\relax +\contentsline {part}{I\hspace {1em}Feed Storage Module}{2}{part.1}% +\etoc@startlocaltoc {1} +\contentsline {section}{\numberline {I.}Module Introduction}{5}{section.1}% +\contentsline {subsection}{\numberline {A.}Feed Quality Assessment}{5}{subsection.1.1}% +\contentsline {section}{\numberline {II.}Feed Storage Inputs}{6}{section.2}% +\contentsline {section}{\numberline {III.}Storage Classifications}{6}{section.3}% +\contentsline {subsection}{\numberline {A.}Grain}{6}{subsection.3.1}% +\contentsline {subsection}{\numberline {B.}Hay}{7}{subsection.3.2}% +\contentsline {subsection}{\numberline {C.}Silage}{9}{subsection.3.3}% +\contentsline {subsection}{\numberline {D.}Baleage}{12}{subsection.3.4}% +\contentsline {subsection}{\numberline {E.}Nutrient Composition}{12}{subsection.3.5}% +\contentsline {section}{\numberline {IV.}References}{13}{section.4}% diff --git a/docs/scientific/main.aux b/docs/scientific/main.aux index f7ddb6e563..005adbb605 100644 --- a/docs/scientific/main.aux +++ b/docs/scientific/main.aux @@ -1,14 +1,23 @@ \relax -\providecommand \babel@aux [2]{\global \let \babel@toc \@gobbletwo } +\providecommand\babel@aux[2]{} \@nameuse{bbl@beforestart} \providecommand\hyper@newdestlabel[2]{} \providecommand\HyField@AuxAddToFields[1]{} \providecommand\HyField@AuxAddToCoFields[2]{} -\abx@aux@refcontext{nyt/global//global/global/global} -\@input{animal.aux} +\catcode 95\active +\abx@aux@refcontext{nyt/global//global/global} \@writefile{toc}{\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{}} +\@writefile{toc}{\etoc@setlocaltop \Etoc@part@@ } \babel@aux{english}{} -\abx@aux@refsection{1}{9} +\@writefile{toc}{\contentsline {part}{I\hspace {1em}Preface: A Day in the Life on a RuFaS Farm}{4}{part.1}\protected@file@percent } +\newlabel{rufasday}{{I}{4}{Preface: A Day in the Life on a RuFaS Farm}{part.1}{}} +\@writefile{toc}{\contentsline {paragraph}{Feeding the Animals}{4}{part.1}\protected@file@percent } +\@writefile{toc}{\contentsline {paragraph}{Taking Care of the Animals}{4}{part.1}\protected@file@percent } +\@writefile{toc}{\contentsline {paragraph}{Dealing with the Manure}{5}{part.1}\protected@file@percent } +\@writefile{toc}{\contentsline {paragraph}{Managing the Fields}{5}{part.1}\protected@file@percent } +\@writefile{toc}{\contentsline {paragraph}{Storing the Feeds}{5}{part.1}\protected@file@percent } +\@input{animal.aux} +\abx@aux@refsection{1}{10} \abx@aux@cite{1}{reuven2017} \abx@aux@segm{1}{0}{reuven2017} \abx@aux@page{2}{10} @@ -20,105 +29,105 @@ \abx@aux@segm{1}{0}{nrc2001} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{3}{18} -\abx@aux@page{4}{18} -\abx@aux@page{5}{18} -\abx@aux@page{6}{18} +\abx@aux@page{3}{19} +\abx@aux@page{4}{19} +\abx@aux@page{5}{19} +\abx@aux@page{6}{19} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{7}{30} +\abx@aux@page{7}{31} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{8}{32} +\abx@aux@page{8}{33} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} +\abx@aux@page{9}{36} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{9}{36} -\abx@aux@page{10}{37} +\abx@aux@page{10}{38} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{11}{39} -\abx@aux@page{12}{39} +\abx@aux@page{11}{40} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{13}{40} -\abx@aux@page{14}{41} +\abx@aux@page{12}{41} +\abx@aux@page{13}{41} +\abx@aux@page{14}{42} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{15}{42} \abx@aux@cite{1}{nrc2001} \abx@aux@segm{1}{0}{nrc2001} -\abx@aux@page{16}{43} +\abx@aux@page{15}{44} +\abx@aux@page{16}{44} \abx@aux@cite{1}{nrc2001} \abx@aux@segm{1}{0}{nrc2001} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} \abx@aux@cite{1}{nrc2001} \abx@aux@segm{1}{0}{nrc2001} -\abx@aux@page{17}{45} -\abx@aux@page{18}{45} -\abx@aux@page{19}{45} +\abx@aux@page{17}{46} +\abx@aux@page{18}{46} +\abx@aux@page{19}{46} \abx@aux@cite{1}{nrc2021} \abx@aux@segm{1}{0}{nrc2021} -\abx@aux@page{20}{48} +\abx@aux@page{20}{49} \abx@aux@cite{1}{nrc2001} \abx@aux@segm{1}{0}{nrc2001} -\abx@aux@page{21}{51} +\abx@aux@page{21}{52} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} -\abx@aux@page{22}{53} +\abx@aux@page{22}{54} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} -\abx@aux@page{23}{55} +\abx@aux@page{23}{58} \abx@aux@cite{1}{reuven2017} \abx@aux@segm{1}{0}{reuven2017} -\abx@aux@page{24}{59} +\abx@aux@page{24}{62} \abx@aux@cite{1}{Li2023} \abx@aux@segm{1}{0}{Li2023} -\abx@aux@page{25}{60} +\abx@aux@page{25}{64} \abx@aux@cite{1}{nrc2001} \abx@aux@segm{1}{0}{nrc2001} -\abx@aux@page{26}{62} +\abx@aux@page{26}{65} \abx@aux@cite{1}{Korver1985} \abx@aux@segm{1}{0}{Korver1985} -\abx@aux@page{27}{63} \abx@aux@cite{1}{Galvao2013} \abx@aux@segm{1}{0}{Galvao2013} -\abx@aux@page{28}{64} +\abx@aux@page{27}{67} +\abx@aux@page{28}{67} \abx@aux@cite{1}{dcrc_protocols} \abx@aux@segm{1}{0}{dcrc_protocols} -\abx@aux@page{29}{65} +\abx@aux@page{29}{68} \abx@aux@cite{1}{devries2006} \abx@aux@segm{1}{0}{devries2006} -\abx@aux@page{30}{70} +\abx@aux@page{30}{74} \abx@aux@cite{1}{kalantari2015using} \abx@aux@segm{1}{0}{kalantari2015using} +\abx@aux@page{31}{75} \abx@aux@cite{1}{wiltbank2016} \abx@aux@segm{1}{0}{wiltbank2016} \abx@aux@cite{1}{wiltbank2016} \abx@aux@segm{1}{0}{wiltbank2016} -\abx@aux@page{31}{71} -\abx@aux@page{32}{73} -\abx@aux@page{33}{73} +\abx@aux@page{32}{77} +\abx@aux@page{33}{77} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} -\abx@aux@page{35}{85} +\abx@aux@page{35}{90} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} -\abx@aux@page{36}{88} +\abx@aux@page{36}{93} \abx@aux@cite{1}{Li2022} \abx@aux@segm{1}{0}{Li2022} -\abx@aux@page{37}{89} +\abx@aux@page{37}{94} \abx@aux@cite{1}{Wood1967} \abx@aux@segm{1}{0}{Wood1967} -\abx@aux@page{38}{90} +\abx@aux@page{38}{95} \abx@aux@cite{1}{Hanson2024} \abx@aux@segm{1}{0}{Hanson2024} \abx@aux@cite{1}{reed2015} @@ -155,11 +164,11 @@ \abx@aux@segm{1}{0}{Niu2018} \abx@aux@cite{1}{Pattanaik2003} \abx@aux@segm{1}{0}{Pattanaik2003} -\abx@aux@page{39}{109} -\abx@aux@page{40}{110} -\abx@aux@page{41}{110} -\abx@aux@page{42}{110} -\abx@aux@page{43}{110} +\abx@aux@page{39}{114} +\abx@aux@page{40}{115} +\abx@aux@page{41}{115} +\abx@aux@page{42}{115} +\abx@aux@page{43}{115} \abx@aux@cite{1}{Pattanaik2003} \abx@aux@segm{1}{0}{Pattanaik2003} \abx@aux@cite{1}{Niu2018} @@ -168,48 +177,48 @@ \abx@aux@segm{1}{0}{Niu2018} \abx@aux@cite{1}{Mills2003} \abx@aux@segm{1}{0}{Mills2003} +\abx@aux@page{44}{117} \abx@aux@cite{1}{Niu2018} \abx@aux@segm{1}{0}{Niu2018} -\abx@aux@page{44}{112} -\abx@aux@page{45}{112} \abx@aux@cite{1}{Mills2003} \abx@aux@segm{1}{0}{Mills2003} \abx@aux@cite{1}{Niu2018} \abx@aux@segm{1}{0}{Niu2018} -\abx@aux@page{46}{113} +\abx@aux@page{45}{118} +\abx@aux@page{46}{118} \abx@aux@cite{1}{Kebreab2023} \abx@aux@segm{1}{0}{Kebreab2023} -\abx@aux@page{47}{118} -\abx@aux@page{48}{118} -\abx@aux@page{49}{118} -\abx@aux@page{50}{118} -\abx@aux@page{51}{118} -\abx@aux@page{52}{118} -\abx@aux@page{53}{118} -\abx@aux@page{54}{118} -\abx@aux@page{55}{118} -\abx@aux@page{56}{118} -\abx@aux@page{57}{118} -\abx@aux@page{58}{118} -\abx@aux@page{59}{118} -\abx@aux@page{60}{118} -\abx@aux@page{61}{118} -\abx@aux@page{62}{118} -\abx@aux@page{63}{118} -\abx@aux@page{64}{118} -\abx@aux@page{65}{118} -\abx@aux@page{66}{118} -\abx@aux@page{67}{118} -\abx@aux@page{68}{119} -\abx@aux@page{69}{119} -\abx@aux@page{70}{119} -\abx@aux@page{71}{119} -\abx@aux@page{72}{119} -\abx@aux@page{73}{119} -\abx@aux@page{74}{119} -\abx@aux@page{75}{119} +\abx@aux@page{47}{122} +\abx@aux@page{48}{122} +\abx@aux@page{49}{122} +\abx@aux@page{50}{122} +\abx@aux@page{51}{122} +\abx@aux@page{52}{122} +\abx@aux@page{53}{122} +\abx@aux@page{54}{122} +\abx@aux@page{55}{122} +\abx@aux@page{56}{122} +\abx@aux@page{57}{122} +\abx@aux@page{58}{122} +\abx@aux@page{59}{122} +\abx@aux@page{60}{122} +\abx@aux@page{61}{122} +\abx@aux@page{62}{122} +\abx@aux@page{63}{122} +\abx@aux@page{64}{122} +\abx@aux@page{65}{122} +\abx@aux@page{66}{122} +\abx@aux@page{67}{122} +\abx@aux@page{68}{123} +\abx@aux@page{69}{123} +\abx@aux@page{70}{123} +\abx@aux@page{71}{123} +\abx@aux@page{72}{123} +\abx@aux@page{73}{123} +\abx@aux@page{74}{123} +\abx@aux@page{75}{123} \@input{manure.aux} -\abx@aux@refsection{2}{7} +\abx@aux@refsection{2}{128} \abx@aux@cite{2}{gomez2010time} \abx@aux@segm{2}{0}{gomez2010time} \abx@aux@cite{2}{espejo2007herd} @@ -226,41 +235,41 @@ \abx@aux@segm{2}{0}{gomez2010time} \abx@aux@cite{2}{Bucklin2009} \abx@aux@segm{2}{0}{Bucklin2009} -\abx@aux@page{83}{22} +\abx@aux@page{76}{144} \abx@aux@cite{2}{Rotz2023} \abx@aux@segm{2}{0}{Rotz2023} \abx@aux@cite{2}{Chianese2009a} \abx@aux@segm{2}{0}{Chianese2009a} -\abx@aux@page{84}{24} -\abx@aux@page{85}{24} +\abx@aux@page{77}{145} +\abx@aux@page{78}{145} \abx@aux@cite{2}{Rotz2006} \abx@aux@segm{2}{0}{Rotz2006} \abx@aux@cite{2}{Rotz2006} \abx@aux@segm{2}{0}{Rotz2006} -\abx@aux@page{86}{26} -\abx@aux@page{87}{26} +\abx@aux@page{79}{147} +\abx@aux@page{80}{147} \abx@aux@cite{2}{Hegg1981} \abx@aux@segm{2}{0}{Hegg1981} \abx@aux@cite{2}{Mukhtar1999} \abx@aux@segm{2}{0}{Mukhtar1999} \abx@aux@cite{2}{Varma2021} \abx@aux@segm{2}{0}{Varma2021} -\abx@aux@page{88}{31} -\abx@aux@page{89}{31} -\abx@aux@page{90}{31} +\abx@aux@page{81}{152} +\abx@aux@page{82}{152} +\abx@aux@page{83}{152} \abx@aux@cite{2}{Jorgensen2009} \abx@aux@segm{2}{0}{Jorgensen2009} \abx@aux@cite{2}{Fournel2019} \abx@aux@segm{2}{0}{Fournel2019} \abx@aux@cite{2}{Fernandez2015} \abx@aux@segm{2}{0}{Fernandez2015} -\abx@aux@page{93}{37} +\abx@aux@page{86}{158} \abx@aux@cite{2}{AguirreVillegas2019} \abx@aux@segm{2}{0}{AguirreVillegas2019} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{94}{41} -\abx@aux@page{95}{41} +\abx@aux@page{87}{162} +\abx@aux@page{88}{162} \abx@aux@cite{2}{Sommer2004} \abx@aux@segm{2}{0}{Sommer2004} \abx@aux@cite{2}{Sommer2004} @@ -273,12 +282,12 @@ \abx@aux@segm{2}{0}{Petersen2024} \abx@aux@cite{2}{Elsgaard2016} \abx@aux@segm{2}{0}{Elsgaard2016} -\abx@aux@page{96}{47} -\abx@aux@page{97}{47} -\abx@aux@page{98}{47} -\abx@aux@page{99}{47} -\abx@aux@page{100}{47} -\abx@aux@page{101}{47} +\abx@aux@page{89}{168} +\abx@aux@page{90}{168} +\abx@aux@page{91}{168} +\abx@aux@page{92}{168} +\abx@aux@page{93}{168} +\abx@aux@page{94}{168} \abx@aux@cite{2}{wallaceDMI} \abx@aux@segm{2}{0}{wallaceDMI} \abx@aux@cite{2}{Petersen2024} @@ -287,25 +296,24 @@ \abx@aux@segm{2}{0}{Petersen2024} \abx@aux@cite{2}{Petersen2024} \abx@aux@segm{2}{0}{Petersen2024} -\abx@aux@page{102}{48} -\abx@aux@page{103}{48} -\abx@aux@page{104}{48} +\abx@aux@page{95}{169} +\abx@aux@page{96}{169} \abx@aux@cite{2}{Rotz2006} \abx@aux@segm{2}{0}{Rotz2006} \abx@aux@cite{2}{Rotz2023} \abx@aux@segm{2}{0}{Rotz2023} -\abx@aux@page{105}{49} -\abx@aux@page{106}{49} -\abx@aux@page{107}{49} +\abx@aux@page{97}{170} +\abx@aux@page{98}{170} +\abx@aux@page{99}{170} \abx@aux@cite{2}{IPCC2019} \abx@aux@segm{2}{0}{IPCC2019} \abx@aux@cite{2}{IPCC2006} \abx@aux@segm{2}{0}{IPCC2006} -\abx@aux@page{108}{50} -\abx@aux@page{109}{51} +\abx@aux@page{100}{171} +\abx@aux@page{101}{172} \abx@aux@cite{2}{NRCS2017} \abx@aux@segm{2}{0}{NRCS2017} -\abx@aux@page{110}{53} +\abx@aux@page{102}{174} \abx@aux@cite{2}{Sommer2004} \abx@aux@segm{2}{0}{Sommer2004} \abx@aux@cite{2}{Sommer2022} @@ -318,188 +326,169 @@ \abx@aux@segm{2}{0}{Petersen2024} \abx@aux@cite{2}{Elsgaard2016} \abx@aux@segm{2}{0}{Elsgaard2016} -\abx@aux@page{111}{57} -\abx@aux@page{112}{57} -\abx@aux@page{113}{57} -\abx@aux@page{114}{57} -\abx@aux@page{115}{57} -\abx@aux@page{116}{57} +\abx@aux@page{103}{178} +\abx@aux@page{104}{178} +\abx@aux@page{105}{178} +\abx@aux@page{106}{178} \abx@aux@cite{2}{Petersen2024} \abx@aux@segm{2}{0}{Petersen2024} \abx@aux@cite{2}{Petersen2024} \abx@aux@segm{2}{0}{Petersen2024} +\abx@aux@page{107}{179} +\abx@aux@page{108}{179} \abx@aux@cite{2}{Petersen2024} \abx@aux@segm{2}{0}{Petersen2024} -\abx@aux@page{117}{58} -\abx@aux@page{118}{58} \abx@aux@cite{2}{Rotz2006} \abx@aux@segm{2}{0}{Rotz2006} \abx@aux@cite{2}{Rotz2023} \abx@aux@segm{2}{0}{Rotz2023} -\abx@aux@page{119}{59} -\abx@aux@page{120}{59} -\abx@aux@page{121}{59} +\abx@aux@page{109}{180} +\abx@aux@page{110}{180} +\abx@aux@page{111}{180} +\abx@aux@page{112}{181} +\abx@aux@page{113}{181} \abx@aux@cite{2}{IPCC2019} \abx@aux@segm{2}{0}{IPCC2019} -\abx@aux@page{122}{61} +\abx@aux@page{114}{182} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} \abx@aux@cite{2}{bonifacio2017a} \abx@aux@segm{2}{0}{bonifacio2017a} \abx@aux@cite{2}{bonifacio2017b} \abx@aux@segm{2}{0}{bonifacio2017b} -\abx@aux@page{123}{66} -\abx@aux@page{124}{67} -\abx@aux@page{125}{67} +\abx@aux@page{115}{187} +\abx@aux@page{116}{188} +\abx@aux@page{117}{188} \abx@aux@cite{2}{larney2011} \abx@aux@segm{2}{0}{larney2011} -\abx@aux@page{126}{68} +\abx@aux@page{118}{189} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{127}{70} +\abx@aux@page{119}{191} \abx@aux@cite{2}{Rotz2023} \abx@aux@segm{2}{0}{Rotz2023} \abx@aux@cite{2}{IPCC2006} \abx@aux@segm{2}{0}{IPCC2006} -\abx@aux@page{128}{76} -\abx@aux@page{129}{76} +\abx@aux@page{120}{197} +\abx@aux@page{121}{197} \abx@aux@cite{2}{bonifacio2017a} \abx@aux@segm{2}{0}{bonifacio2017a} \abx@aux@cite{2}{bonifacio2017b} \abx@aux@segm{2}{0}{bonifacio2017b} -\abx@aux@page{130}{77} -\abx@aux@page{131}{77} +\abx@aux@page{122}{198} +\abx@aux@page{123}{198} \abx@aux@cite{2}{larney2011} \abx@aux@segm{2}{0}{larney2011} -\abx@aux@page{132}{78} +\abx@aux@page{124}{199} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{133}{80} -\abx@aux@page{134}{80} +\abx@aux@page{125}{201} +\abx@aux@page{126}{201} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{135}{81} +\abx@aux@page{127}{202} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} \abx@aux@cite{2}{bonifacio2017a} \abx@aux@segm{2}{0}{bonifacio2017a} \abx@aux@cite{2}{bonifacio2017b} \abx@aux@segm{2}{0}{bonifacio2017b} -\abx@aux@page{136}{86} -\abx@aux@page{137}{87} -\abx@aux@page{138}{87} +\abx@aux@page{128}{207} +\abx@aux@page{129}{208} +\abx@aux@page{130}{208} \abx@aux@cite{2}{larney2011} \abx@aux@segm{2}{0}{larney2011} -\abx@aux@page{139}{88} +\abx@aux@page{131}{209} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{140}{89} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} +\abx@aux@page{132}{211} +\abx@aux@page{133}{211} \abx@aux@cite{2}{Hanson2024} \abx@aux@segm{2}{0}{Hanson2024} -\abx@aux@page{141}{90} -\abx@aux@page{142}{90} +\abx@aux@page{134}{212} \abx@aux@cite{2}{Petersen2024} \abx@aux@segm{2}{0}{Petersen2024} -\abx@aux@page{143}{98} -\abx@aux@page{144}{102} -\abx@aux@page{145}{102} -\abx@aux@page{146}{102} -\abx@aux@page{147}{102} -\abx@aux@page{148}{102} -\abx@aux@page{149}{102} -\abx@aux@page{150}{102} -\abx@aux@page{151}{102} -\abx@aux@page{152}{102} -\abx@aux@page{153}{102} -\abx@aux@page{154}{102} -\abx@aux@page{155}{102} -\abx@aux@page{156}{102} -\abx@aux@page{157}{102} -\abx@aux@page{158}{102} -\abx@aux@page{159}{102} -\abx@aux@page{160}{102} -\abx@aux@page{161}{102} -\abx@aux@page{162}{102} -\abx@aux@page{163}{103} -\abx@aux@page{164}{103} -\abx@aux@page{165}{103} -\abx@aux@page{166}{103} -\abx@aux@page{167}{103} -\abx@aux@page{168}{103} -\abx@aux@page{169}{103} -\abx@aux@page{170}{103} -\abx@aux@page{171}{103} +\abx@aux@page{135}{221} +\abx@aux@page{136}{224} +\abx@aux@page{137}{224} +\abx@aux@page{138}{224} +\abx@aux@page{139}{224} +\abx@aux@page{140}{224} +\abx@aux@page{141}{224} +\abx@aux@page{142}{224} +\abx@aux@page{143}{224} +\abx@aux@page{144}{224} +\abx@aux@page{145}{224} +\abx@aux@page{146}{224} +\abx@aux@page{147}{224} +\abx@aux@page{148}{224} +\abx@aux@page{149}{224} +\abx@aux@page{150}{224} +\abx@aux@page{151}{224} +\abx@aux@page{152}{224} +\abx@aux@page{153}{224} +\abx@aux@page{154}{224} +\abx@aux@page{155}{225} +\abx@aux@page{156}{225} +\abx@aux@page{157}{225} \@input{crop_and_soil.aux} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{172}{20} -\abx@aux@page{173}{20} +\abx@aux@page{158}{242} +\abx@aux@page{159}{242} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{174}{22} +\abx@aux@page{160}{243} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{175}{24} +\abx@aux@page{161}{245} \abx@aux@cite{0}{hargreaves1985} \abx@aux@segm{0}{0}{hargreaves1985} -\abx@aux@page{176}{32} \abx@aux@cite{0}{mu-extsoil} \abx@aux@segm{0}{0}{mu-extsoil} -\abx@aux@page{177}{42} \abx@aux@cite{0}{hayes2020vindication} \abx@aux@segm{0}{0}{hayes2020vindication} -\abx@aux@page{178}{49} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{179}{50} +\abx@aux@page{162}{272} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} +\abx@aux@page{163}{273} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{180}{51} -\abx@aux@page{181}{52} +\abx@aux@page{164}{274} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{182}{53} +\abx@aux@page{165}{275} \abx@aux@cite{0}{vadas2007} \abx@aux@segm{0}{0}{vadas2007} -\abx@aux@page{183}{54} +\abx@aux@page{166}{277} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{184}{65} -\abx@aux@page{185}{65} -\abx@aux@page{186}{65} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{187}{66} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{188}{68} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{189}{69} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{190}{71} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} \abx@aux@cite{0}{parton1987analysis} \abx@aux@segm{0}{0}{parton1987analysis} -\abx@aux@page{191}{72} -\abx@aux@page{192}{72} -\abx@aux@page{193}{72} \abx@aux@cite{0}{fan2016root} \abx@aux@segm{0}{0}{fan2016root} \abx@aux@cite{0}{fan2016root} @@ -510,83 +499,78 @@ \abx@aux@segm{0}{0}{fan2016root} \abx@aux@cite{0}{fan2016root} \abx@aux@segm{0}{0}{fan2016root} -\abx@aux@page{194}{95} -\abx@aux@page{195}{95} -\abx@aux@page{196}{95} -\abx@aux@page{197}{95} -\abx@aux@page{198}{95} -\abx@aux@refsection{3}{97} +\abx@aux@refsection{3}{318} \@input{feed_storage.aux} -\abx@aux@refsection{4}{8} +\abx@aux@refsection{4}{322} \abx@aux@cite{4}{pahlow2003microbiology} \abx@aux@segm{4}{0}{pahlow2003microbiology} \abx@aux@cite{4}{pahlow2003microbiology} \abx@aux@segm{4}{0}{pahlow2003microbiology} \abx@aux@cite{4}{muck2013recent} \abx@aux@segm{4}{0}{muck2013recent} -\abx@aux@page{199}{12} -\abx@aux@page{200}{12} -\abx@aux@page{201}{12} -\abx@aux@page{202}{18} -\abx@aux@page{203}{18} -\abx@aux@read@bbl@mdfivesum{C78D0B6E62ACDCCDD0810A83C482C959} -\abx@aux@defaultrefcontext{1}{appuhamy2014}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{appuhamy2018}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{asabe2005}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{boadi2004}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{deboer2002a}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{dcrc_protocols}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{devries2006}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Galvao2013}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Hanson2024}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{IPCC2006}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{johnson2016}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{kalantari2015using}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Kebreab2023}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Korver1985}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Li2023}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Li2022}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Mills2003}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{monteny2002b}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{nrc2021}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{nrc2001}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{nennich2005}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Niu2018}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Pattanaik2003}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{reed2015}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{reuven2017}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{vadas2007}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{wilkerson1997prediction}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{wiltbank2016}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{1}{Wood1967}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{AguirreVillegas2019}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{bonifacio2017a}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{bonifacio2017b}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Bucklin2009}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Chianese2009a}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Elsgaard2016}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{endres2007behavior}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{espejo2007herd}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Fernandez2015}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Fournel2019}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{gomez2010time}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Hanson2024}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Hegg1981}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{IPCC2019}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{IPCC2006}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{jewell2019prevalence}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Jorgensen2009}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{larney2011}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{meyer2019contract}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Mukhtar1999}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{NRCS2017}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Petersen2024}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Rotz2023}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Rotz2006}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Sommer2022}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Sommer2004}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{Varma2021}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{2}{wallaceDMI}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{4}{muck2013recent}{nyt/global//global/global/global} -\abx@aux@defaultrefcontext{4}{pahlow2003microbiology}{nyt/global//global/global/global} -\gdef \@abspage@last{341} +\abx@aux@page{167}{326} +\abx@aux@page{168}{326} +\abx@aux@page{169}{326} +\abx@aux@page{170}{330} +\abx@aux@page{171}{330} +\gdef \LT@liii {\LT@entry + {1}{108.18068pt}\LT@entry + {1}{321.07614pt}} +\@writefile{toc}{\contentsline {part}{VI\hspace {1em}Abbreviations}{331}{part.6}\protected@file@percent } +\@writefile{toc}{\contentsline {table}{\numberline {95}{\ignorespaces Common abbreviations used throughout this document}}{331}{table.95}\protected@file@percent } +\@writefile{lot}{\contentsline {table}{\numberline {95}{\ignorespaces Common abbreviations used throughout this document}}{331}{table.95}\protected@file@percent } +\abx@aux@read@bbl@mdfivesum{D2E78B893CDDD7C8A4450A50C1678394} +\abx@aux@defaultrefcontext{1}{appuhamy2014}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{appuhamy2018}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{asabe2005}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{boadi2004}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{deboer2002a}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{dcrc_protocols}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{devries2006}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Galvao2013}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Hanson2024}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{IPCC2006}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{johnson2016}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{kalantari2015using}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Kebreab2023}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Korver1985}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Li2023}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Li2022}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Mills2003}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{monteny2002b}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{nrc2021}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{nrc2001}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{nennich2005}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Niu2018}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Pattanaik2003}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{reed2015}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{reuven2017}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{vadas2007}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{wilkerson1997prediction}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{wiltbank2016}{nyt/global//global/global} +\abx@aux@defaultrefcontext{1}{Wood1967}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{AguirreVillegas2019}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{bonifacio2017a}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{bonifacio2017b}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Bucklin2009}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Chianese2009a}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Elsgaard2016}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Fernandez2015}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Fournel2019}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Hanson2024}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Hegg1981}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{IPCC2019}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{IPCC2006}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Jorgensen2009}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{larney2011}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Mukhtar1999}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{NRCS2017}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Petersen2024}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Rotz2023}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Rotz2006}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Sommer2022}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Sommer2004}{nyt/global//global/global} +\abx@aux@defaultrefcontext{2}{Varma2021}{nyt/global//global/global} +\abx@aux@defaultrefcontext{4}{muck2013recent}{nyt/global//global/global} +\abx@aux@defaultrefcontext{4}{pahlow2003microbiology}{nyt/global//global/global} +\gdef \@abspage@last{333} diff --git a/docs/scientific/main.bbl b/docs/scientific/main.bbl index 0079f7caf1..e78575d8ef 100644 --- a/docs/scientific/main.bbl +++ b/docs/scientific/main.bbl @@ -1,5 +1,5 @@ % $ biblatex auxiliary file $ -% $ biblatex bbl format version 3.3 $ +% $ biblatex bbl format version 3.2 $ % Do not modify the above lines! % % This is an auxiliary file used by the 'biblatex' package. @@ -18,228 +18,8 @@ \refsection{0} - \datalist[entry]{nyt/global//global/global/global} - \entry{fan2016root}{article}{}{} - \name{author}{4}{}{% - {{un=0,uniquepart=base,hash=e15b815678e316512682ce6a40bdf834}{% - family={Fan}, - familyi={F\bibinitperiod}, - given={J.}, - giveni={J\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=71e1badf8f17eed2e3654620cc39ee91}{% - family={McConkey}, - familyi={M\bibinitperiod}, - given={B.}, - giveni={B\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=39856f0439f35f79a8eed8b12d26166c}{% - family={Wang}, - familyi={W\bibinitperiod}, - given={H.}, - giveni={H\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=1253fa8df868f86981529392cea69682}{% - family={Janzen}, - familyi={J\bibinitperiod}, - given={H.}, - giveni={H\bibinitperiod}, - givenun=0}}% - } - \strng{namehash}{32217b75420aafa58aba0cb675133e95} - \strng{fullhash}{d3caf10cab02de4069b53b462bd67037} - \strng{fullhashraw}{d3caf10cab02de4069b53b462bd67037} - \strng{bibnamehash}{32217b75420aafa58aba0cb675133e95} - \strng{authorbibnamehash}{32217b75420aafa58aba0cb675133e95} - \strng{authornamehash}{32217b75420aafa58aba0cb675133e95} - \strng{authorfullhash}{d3caf10cab02de4069b53b462bd67037} - \strng{authorfullhashraw}{d3caf10cab02de4069b53b462bd67037} - \field{sortinit}{F} - \field{sortinithash}{2638baaa20439f1b5a8f80c6c08a13b4} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Field Crops Research} - \field{title}{Root distribution by depth for temperate agricultural crops} - \field{volume}{189} - \field{year}{2016} - \field{pages}{68\bibrangedash 74} - \range{pages}{7} - \verb{doi} - \verb 10.1016/j.fcr.2016.02.013 - \endverb - \verb{urlraw} - \verb https://doi.org/10.1016/j.fcr.2016.02.013 - \endverb - \verb{url} - \verb https://doi.org/10.1016/j.fcr.2016.02.013 - \endverb - \endentry - \entry{hargreaves1985}{article}{}{} - \name{author}{2}{}{% - {{un=0,uniquepart=base,hash=3a2a388386dde5b212c7bc77ac0322a1}{% - family={Hargreaves}, - familyi={H\bibinitperiod}, - given={George\bibnamedelima H}, - giveni={G\bibinitperiod\bibinitdelim H\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=28a955da7b11477bd50b1497d29c6c65}{% - family={Samani}, - familyi={S\bibinitperiod}, - given={Zohrab\bibnamedelima A}, - giveni={Z\bibinitperiod\bibinitdelim A\bibinitperiod}, - givenun=0}}% - } - \list{publisher}{2}{% - {American Society of Agricultural}% - {Biological Engineers}% - } - \strng{namehash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{fullhash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{fullhashraw}{6a005ece0e24afb8d7049a7715127ccf} - \strng{bibnamehash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{authorbibnamehash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{authornamehash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{authorfullhash}{6a005ece0e24afb8d7049a7715127ccf} - \strng{authorfullhashraw}{6a005ece0e24afb8d7049a7715127ccf} - \field{sortinit}{H} - \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Applied engineering in agriculture} - \field{number}{2} - \field{title}{Reference crop evapotranspiration from temperature} - \field{volume}{1} - \field{year}{1985} - \field{pages}{96\bibrangedash 99} - \range{pages}{4} - \endentry - \entry{hayes2020vindication}{article}{}{} - \name{author}{2}{}{% - {{un=0,uniquepart=base,hash=5dd552c2d4b881bbc95f627fa9135674}{% - family={Hayes}, - familyi={H\bibinitperiod}, - given={Michael\bibnamedelima HB}, - giveni={M\bibinitperiod\bibinitdelim H\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=d821ecc66c8d49b7cd72446dbe2e0401}{% - family={Swift}, - familyi={S\bibinitperiod}, - given={Roger\bibnamedelima S}, - giveni={R\bibinitperiod\bibinitdelim S\bibinitperiod}, - givenun=0}}% - } - \list{publisher}{1}{% - {Elsevier}% - } - \strng{namehash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{fullhash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{fullhashraw}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{bibnamehash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{authorbibnamehash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{authornamehash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{authorfullhash}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \strng{authorfullhashraw}{84cfe520b0c19ee9a9b9f57c46b81bd1} - \field{sortinit}{H} - \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Advances in Agronomy} - \field{title}{Vindication of humic substances as a key component of organic matter in soil and water} - \field{volume}{163} - \field{year}{2020} - \field{pages}{1\bibrangedash 37} - \range{pages}{37} - \endentry - \entry{parton1987analysis}{article}{}{} - \name{author}{4}{}{% - {{un=0,uniquepart=base,hash=d58df4e21e80b2447195fce112543606}{% - family={Parton}, - familyi={P\bibinitperiod}, - given={William\bibnamedelima J}, - giveni={W\bibinitperiod\bibinitdelim J\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=dbfe95e1245daea08d73cf1751adfefd}{% - family={Schimel}, - familyi={S\bibinitperiod}, - given={David\bibnamedelima S}, - giveni={D\bibinitperiod\bibinitdelim S\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=dee55c05f3e8c17c04f1df32a40854f1}{% - family={Cole}, - familyi={C\bibinitperiod}, - given={C\bibnamedelima Vernon}, - giveni={C\bibinitperiod\bibinitdelim V\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=c54c6a3bfbd13442eeaabc6b36616a35}{% - family={Ojima}, - familyi={O\bibinitperiod}, - given={Dennis\bibnamedelima S}, - giveni={D\bibinitperiod\bibinitdelim S\bibinitperiod}, - givenun=0}}% - } - \list{publisher}{1}{% - {Wiley Online Library}% - } - \strng{namehash}{726d1bbc6906df459be95e0989fbc745} - \strng{fullhash}{ab71d409edd2fafe8a527760d1e5345e} - \strng{fullhashraw}{ab71d409edd2fafe8a527760d1e5345e} - \strng{bibnamehash}{726d1bbc6906df459be95e0989fbc745} - \strng{authorbibnamehash}{726d1bbc6906df459be95e0989fbc745} - \strng{authornamehash}{726d1bbc6906df459be95e0989fbc745} - \strng{authorfullhash}{ab71d409edd2fafe8a527760d1e5345e} - \strng{authorfullhashraw}{ab71d409edd2fafe8a527760d1e5345e} - \field{sortinit}{P} - \field{sortinithash}{ff3bcf24f47321b42cb156c2cc8a8422} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Soil Science Society of America Journal} - \field{number}{5} - \field{title}{Analysis of factors controlling soil organic matter levels in Great Plains grasslands} - \field{volume}{51} - \field{year}{1987} - \field{pages}{1173\bibrangedash 1179} - \range{pages}{7} - \endentry - \entry{mu-extsoil}{misc}{}{} - \name{author}{1}{}{% - {{un=0,uniquepart=base,hash=11d8e6e5fb591c74bd9cd6639f136cb1}{% - family={{University of Missouri Extension}}, - familyi={U\bibinitperiod}}}% - } - \strng{namehash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{fullhash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{fullhashraw}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{bibnamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{authorbibnamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{authornamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{authorfullhash}{11d8e6e5fb591c74bd9cd6639f136cb1} - \strng{authorfullhashraw}{11d8e6e5fb591c74bd9cd6639f136cb1} - \field{sortinit}{U} - \field{sortinithash}{6901a00e45705986ee5e7ca9fd39adca} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{howpublished}{Publication WQ257, University of Missouri Extension} - \field{note}{Reviewed November 2022; accessed 2023} - \field{title}{Nitrogen in the Environment: Ammonia Volatilization} - \field{year}{2022} - \verb{urlraw} - \verb https://extension.missouri.edu/publications/wq257 - \endverb - \verb{url} - \verb https://extension.missouri.edu/publications/wq257 - \endverb - \endentry - \entry{vadas2007}{article}{}{} + \datalist[entry]{nyt/global//global/global} + \entry{vadas2007}{article}{} \name{author}{7}{}{% {{un=0,uniquepart=base,hash=0ccd882cd1b35af5e3b66329f8c482b8}{% family={Vadas}, @@ -286,12 +66,10 @@ } \strng{namehash}{678003f4d6d3452a1ae65de262babbfd} \strng{fullhash}{07b9400921c16e88e9116e0e416ff058} - \strng{fullhashraw}{07b9400921c16e88e9116e0e416ff058} \strng{bibnamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authorbibnamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authornamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authorfullhash}{07b9400921c16e88e9116e0e416ff058} - \strng{authorfullhashraw}{07b9400921c16e88e9116e0e416ff058} \field{sortinit}{V} \field{sortinithash}{afb52128e5b4dc4b843768c0113d673b} \field{extradatescope}{labelyear} @@ -307,11 +85,16 @@ \range{pages}{9} \endentry \enddatalist + \missing{fan2016root} + \missing{hargreaves1985} + \missing{hayes2020vindication} + \missing{mu-extsoil} + \missing{parton1987analysis} \endrefsection \refsection{1} - \datalist[entry]{nyt/global//global/global/global} - \entry{appuhamy2014}{article}{}{} + \datalist[entry]{nyt/global//global/global} + \entry{appuhamy2014}{article}{} \name{author}{6}{ul=5}{% {{un=0,uniquepart=base,hash=31329d77405a1749191d9c0cf4b61302}{% family={Appuhamy}, @@ -352,12 +135,10 @@ } \strng{namehash}{b8065ee8fc02a89459a8e38347dc0dc3} \strng{fullhash}{c1df9e5c354c967026f7f208fddafc49} - \strng{fullhashraw}{c1df9e5c354c967026f7f208fddafc49} \strng{bibnamehash}{b8065ee8fc02a89459a8e38347dc0dc3} \strng{authorbibnamehash}{b8065ee8fc02a89459a8e38347dc0dc3} \strng{authornamehash}{b8065ee8fc02a89459a8e38347dc0dc3} \strng{authorfullhash}{c1df9e5c354c967026f7f208fddafc49} - \strng{authorfullhashraw}{c1df9e5c354c967026f7f208fddafc49} \field{sortinit}{A} \field{sortinithash}{2f401846e2029bad6b3ecc16d50031e2} \field{extradatescope}{labelyear} @@ -371,7 +152,7 @@ \field{year}{2014} \true{nocite} \endentry - \entry{appuhamy2018}{article}{}{} + \entry{appuhamy2018}{article}{} \name{author}{5}{ul=5}{% {{un=0,uniquepart=base,hash=31329d77405a1749191d9c0cf4b61302}{% family={Appuhamy}, @@ -406,12 +187,10 @@ } \strng{namehash}{e26f640b917ae632cf4c80d42f7f934e} \strng{fullhash}{e26f640b917ae632cf4c80d42f7f934e} - \strng{fullhashraw}{e26f640b917ae632cf4c80d42f7f934e} \strng{bibnamehash}{e26f640b917ae632cf4c80d42f7f934e} \strng{authorbibnamehash}{e26f640b917ae632cf4c80d42f7f934e} \strng{authornamehash}{e26f640b917ae632cf4c80d42f7f934e} \strng{authorfullhash}{e26f640b917ae632cf4c80d42f7f934e} - \strng{authorfullhashraw}{e26f640b917ae632cf4c80d42f7f934e} \field{sortinit}{A} \field{sortinithash}{2f401846e2029bad6b3ecc16d50031e2} \field{extradatescope}{labelyear} @@ -427,7 +206,7 @@ \field{pages}{820\bibrangedash 829} \range{pages}{10} \endentry - \entry{asabe2005}{book}{}{} + \entry{asabe2005}{book}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=ba9b352c5e4e27810b1e3a2aadb0c337}{% family={{ASABE}}, @@ -441,12 +220,10 @@ } \strng{namehash}{ba9b352c5e4e27810b1e3a2aadb0c337} \strng{fullhash}{ba9b352c5e4e27810b1e3a2aadb0c337} - \strng{fullhashraw}{ba9b352c5e4e27810b1e3a2aadb0c337} \strng{bibnamehash}{ba9b352c5e4e27810b1e3a2aadb0c337} \strng{authorbibnamehash}{ba9b352c5e4e27810b1e3a2aadb0c337} \strng{authornamehash}{ba9b352c5e4e27810b1e3a2aadb0c337} \strng{authorfullhash}{ba9b352c5e4e27810b1e3a2aadb0c337} - \strng{authorfullhashraw}{ba9b352c5e4e27810b1e3a2aadb0c337} \field{sortinit}{A} \field{sortinithash}{2f401846e2029bad6b3ecc16d50031e2} \field{extradatescope}{labelyear} @@ -459,7 +236,7 @@ \field{pages}{1\bibrangedash 32} \range{pages}{32} \endentry - \entry{boadi2004}{article}{}{} + \entry{boadi2004}{article}{} \name{author}{4}{}{% {{un=0,uniquepart=base,hash=6552fb7c9d573192537dbd7ac86f606a}{% family={Boadi}, @@ -488,12 +265,10 @@ } \strng{namehash}{adb15a88ec2ecd2b122cda4a0605f2eb} \strng{fullhash}{09d036fb2b42fbfd59cac487ec0e9a62} - \strng{fullhashraw}{09d036fb2b42fbfd59cac487ec0e9a62} \strng{bibnamehash}{adb15a88ec2ecd2b122cda4a0605f2eb} \strng{authorbibnamehash}{adb15a88ec2ecd2b122cda4a0605f2eb} \strng{authornamehash}{adb15a88ec2ecd2b122cda4a0605f2eb} \strng{authorfullhash}{09d036fb2b42fbfd59cac487ec0e9a62} - \strng{authorfullhashraw}{09d036fb2b42fbfd59cac487ec0e9a62} \field{sortinit}{B} \field{sortinithash}{d7095fff47cda75ca2589920aae98399} \field{extradatescope}{labelyear} @@ -512,7 +287,7 @@ \verb 10.4141/A03-109 \endverb \endentry - \entry{deboer2002a}{article}{}{} + \entry{deboer2002a}{article}{} \name{author}{5}{}{% {{un=0,uniquepart=base,hash=884977aeeeb305da395f4807fa3f0366}{% family={Boer}, @@ -553,12 +328,10 @@ } \strng{namehash}{151d144c419ef3cbf1eed2d1736ffe8c} \strng{fullhash}{8a204d59aa3878862e65729240acbb64} - \strng{fullhashraw}{8a204d59aa3878862e65729240acbb64} \strng{bibnamehash}{151d144c419ef3cbf1eed2d1736ffe8c} \strng{authorbibnamehash}{151d144c419ef3cbf1eed2d1736ffe8c} \strng{authornamehash}{151d144c419ef3cbf1eed2d1736ffe8c} \strng{authorfullhash}{8a204d59aa3878862e65729240acbb64} - \strng{authorfullhashraw}{8a204d59aa3878862e65729240acbb64} \field{sortinit}{B} \field{sortinithash}{d7095fff47cda75ca2589920aae98399} \field{extradatescope}{labelyear} @@ -577,7 +350,7 @@ \verb 10.3168/jds.S0022-0302(02)74425-1 \endverb \endentry - \entry{dcrc_protocols}{misc}{}{} + \entry{dcrc_protocols}{misc}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=2ce488c6c3b5bfcca538512031c5fc93}{% family={{Dairy Cattle Reproduction Council}}, @@ -585,12 +358,10 @@ } \strng{namehash}{2ce488c6c3b5bfcca538512031c5fc93} \strng{fullhash}{2ce488c6c3b5bfcca538512031c5fc93} - \strng{fullhashraw}{2ce488c6c3b5bfcca538512031c5fc93} \strng{bibnamehash}{2ce488c6c3b5bfcca538512031c5fc93} \strng{authorbibnamehash}{2ce488c6c3b5bfcca538512031c5fc93} \strng{authornamehash}{2ce488c6c3b5bfcca538512031c5fc93} \strng{authorfullhash}{2ce488c6c3b5bfcca538512031c5fc93} - \strng{authorfullhashraw}{2ce488c6c3b5bfcca538512031c5fc93} \field{sortinit}{D} \field{sortinithash}{6f385f66841fb5e82009dc833c761848} \field{extradatescope}{labelyear} @@ -607,7 +378,7 @@ \verb https://www.dcrcouncil.org/protocols/ \endverb \endentry - \entry{devries2006}{article}{}{} + \entry{devries2006}{article}{} \name{author}{6}{}{% {{un=0,uniquepart=base,hash=2e1985593e20bbbc1af4d4427a567da2}{% family={De\bibnamedelima Vries}, @@ -648,12 +419,10 @@ } \strng{namehash}{b92a5eb711d73f48ab3c157bb7b6c738} \strng{fullhash}{837fa8c2fa5a053735f2ba4bcc84a5c6} - \strng{fullhashraw}{837fa8c2fa5a053735f2ba4bcc84a5c6} \strng{bibnamehash}{b92a5eb711d73f48ab3c157bb7b6c738} \strng{authorbibnamehash}{b92a5eb711d73f48ab3c157bb7b6c738} \strng{authornamehash}{b92a5eb711d73f48ab3c157bb7b6c738} \strng{authorfullhash}{837fa8c2fa5a053735f2ba4bcc84a5c6} - \strng{authorfullhashraw}{837fa8c2fa5a053735f2ba4bcc84a5c6} \field{sortinit}{D} \field{sortinithash}{6f385f66841fb5e82009dc833c761848} \field{extradatescope}{labelyear} @@ -668,7 +437,7 @@ \field{pages}{3028\bibrangedash 3037} \range{pages}{10} \endentry - \entry{Galvao2013}{article}{}{} + \entry{Galvao2013}{article}{} \name{author}{4}{}{% {{un=0,uniquepart=base,hash=5f7e008cc37a59455be1c457cef3373e}{% family={Galvão}, @@ -697,12 +466,10 @@ } \strng{namehash}{2e9eadc5f62f7a056a7e38f4f8b5a478} \strng{fullhash}{1095a78e84f823dfe90a7f2c522aab06} - \strng{fullhashraw}{1095a78e84f823dfe90a7f2c522aab06} \strng{bibnamehash}{2e9eadc5f62f7a056a7e38f4f8b5a478} \strng{authorbibnamehash}{2e9eadc5f62f7a056a7e38f4f8b5a478} \strng{authornamehash}{2e9eadc5f62f7a056a7e38f4f8b5a478} \strng{authorfullhash}{1095a78e84f823dfe90a7f2c522aab06} - \strng{authorfullhashraw}{1095a78e84f823dfe90a7f2c522aab06} \field{sortinit}{G} \field{sortinithash}{32d67eca0634bf53703493fb1090a2e8} \field{extradatescope}{labelyear} @@ -717,7 +484,7 @@ \field{pages}{2681\bibrangedash 2693} \range{pages}{13} \endentry - \entry{Hanson2024}{book}{}{} + \entry{Hanson2024}{book}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=35e0ba836b7e802e2dc667e54f37c852}{% family={Hanson}, @@ -743,12 +510,10 @@ } \strng{namehash}{bd66932f699665f7f17ec408c0785681} \strng{fullhash}{bd66932f699665f7f17ec408c0785681} - \strng{fullhashraw}{bd66932f699665f7f17ec408c0785681} \strng{bibnamehash}{bd66932f699665f7f17ec408c0785681} \strng{authorbibnamehash}{bd66932f699665f7f17ec408c0785681} \strng{authornamehash}{bd66932f699665f7f17ec408c0785681} \strng{authorfullhash}{bd66932f699665f7f17ec408c0785681} - \strng{authorfullhashraw}{bd66932f699665f7f17ec408c0785681} \field{sortinit}{H} \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} \field{extradatescope}{labelyear} @@ -759,7 +524,7 @@ \field{title}{Quantifying Greenhouse Gas Fluxes in Agriculture and Forestry: Methods for Entity-Scale Inventory} \field{year}{2024} \endentry - \entry{IPCC2006}{misc}{}{} + \entry{IPCC2006}{misc}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=676f7b9b8e5bb30500c01e2385e59174}{% family={{IPCC}}, @@ -767,12 +532,10 @@ } \strng{namehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{fullhash}{676f7b9b8e5bb30500c01e2385e59174} - \strng{fullhashraw}{676f7b9b8e5bb30500c01e2385e59174} \strng{bibnamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authorbibnamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authornamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authorfullhash}{676f7b9b8e5bb30500c01e2385e59174} - \strng{authorfullhashraw}{676f7b9b8e5bb30500c01e2385e59174} \field{sortinit}{I} \field{sortinithash}{8d291c51ee89b6cd86bf5379f0b151d8} \field{extradatescope}{labelyear} @@ -784,7 +547,7 @@ \field{title}{Guidelines for National Greenhouse Gas Inventories} \field{year}{2006} \endentry - \entry{johnson2016}{article}{}{} + \entry{johnson2016}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=0a1ae6928ed09b35abd479806bc511c6}{% family={Johnson}, @@ -807,12 +570,10 @@ } \strng{namehash}{7f605501daae507463585ef5ec4dd7e8} \strng{fullhash}{7f605501daae507463585ef5ec4dd7e8} - \strng{fullhashraw}{7f605501daae507463585ef5ec4dd7e8} \strng{bibnamehash}{7f605501daae507463585ef5ec4dd7e8} \strng{authorbibnamehash}{7f605501daae507463585ef5ec4dd7e8} \strng{authornamehash}{7f605501daae507463585ef5ec4dd7e8} \strng{authorfullhash}{7f605501daae507463585ef5ec4dd7e8} - \strng{authorfullhashraw}{7f605501daae507463585ef5ec4dd7e8} \field{sortinit}{J} \field{sortinithash}{b2f54a9081ace9966a7cb9413811edb4} \field{extradatescope}{labelyear} @@ -831,7 +592,7 @@ \verb 10.3168/jds.2015-10730 \endverb \endentry - \entry{kalantari2015using}{book}{}{} + \entry{kalantari2015using}{book}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=886114540c3c0d6a8eafd796d1652ca9}{% family={Kalantari}, @@ -845,12 +606,10 @@ } \strng{namehash}{886114540c3c0d6a8eafd796d1652ca9} \strng{fullhash}{886114540c3c0d6a8eafd796d1652ca9} - \strng{fullhashraw}{886114540c3c0d6a8eafd796d1652ca9} \strng{bibnamehash}{886114540c3c0d6a8eafd796d1652ca9} \strng{authorbibnamehash}{886114540c3c0d6a8eafd796d1652ca9} \strng{authornamehash}{886114540c3c0d6a8eafd796d1652ca9} \strng{authorfullhash}{886114540c3c0d6a8eafd796d1652ca9} - \strng{authorfullhashraw}{886114540c3c0d6a8eafd796d1652ca9} \field{sortinit}{K} \field{sortinithash}{c02bf6bff1c488450c352b40f5d853ab} \field{extradatescope}{labelyear} @@ -860,7 +619,7 @@ \field{title}{Using mathematical modeling techniques for optimized dairy herd management and decision making} \field{year}{2015} \endentry - \entry{Kebreab2023}{article}{}{} + \entry{Kebreab2023}{article}{} \name{author}{7}{}{% {{un=2,uniquepart=given,hash=b5ec9ab6b98e8e735bd56adb07cd7a9e}{% family={Kebreab}, @@ -910,12 +669,10 @@ } \strng{namehash}{229bc54dd74cd2424b496588564024ed} \strng{fullhash}{a5a656e56fadf607e3ea33fadb59b555} - \strng{fullhashraw}{a5a656e56fadf607e3ea33fadb59b555} \strng{bibnamehash}{229bc54dd74cd2424b496588564024ed} \strng{authorbibnamehash}{229bc54dd74cd2424b496588564024ed} \strng{authornamehash}{229bc54dd74cd2424b496588564024ed} \strng{authorfullhash}{a5a656e56fadf607e3ea33fadb59b555} - \strng{authorfullhashraw}{a5a656e56fadf607e3ea33fadb59b555} \field{sortinit}{K} \field{sortinithash}{c02bf6bff1c488450c352b40f5d853ab} \field{extradatescope}{labelyear} @@ -934,7 +691,7 @@ \verb 10.3168/jds.2022-22211 \endverb \endentry - \entry{Korver1985}{article}{}{} + \entry{Korver1985}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=a69c8d7fd3db6e423f037a5ea87838db}{% family={Korver}, @@ -960,12 +717,10 @@ } \strng{namehash}{0edbec984b059f90e4b92dda20d47f05} \strng{fullhash}{0edbec984b059f90e4b92dda20d47f05} - \strng{fullhashraw}{0edbec984b059f90e4b92dda20d47f05} \strng{bibnamehash}{0edbec984b059f90e4b92dda20d47f05} \strng{authorbibnamehash}{0edbec984b059f90e4b92dda20d47f05} \strng{authornamehash}{0edbec984b059f90e4b92dda20d47f05} \strng{authorfullhash}{0edbec984b059f90e4b92dda20d47f05} - \strng{authorfullhashraw}{0edbec984b059f90e4b92dda20d47f05} \field{sortinit}{K} \field{sortinithash}{c02bf6bff1c488450c352b40f5d853ab} \field{extradatescope}{labelyear} @@ -980,7 +735,7 @@ \field{pages}{233\bibrangedash 241} \range{pages}{9} \endentry - \entry{Li2023}{article}{}{} + \entry{Li2023}{article}{} \name{author}{5}{ul=2}{% {{un=0,uniquepart=base,hash=32ecf3b8563f881c200eaaf65381ff0d}{% family={Li}, @@ -1015,12 +770,10 @@ } \strng{namehash}{6c72ec468af54298a2900e979cd98605} \strng{fullhash}{6bdaa983dbe01047e2f444ba195a1273} - \strng{fullhashraw}{6bdaa983dbe01047e2f444ba195a1273} \strng{bibnamehash}{6c72ec468af54298a2900e979cd98605} \strng{authorbibnamehash}{6c72ec468af54298a2900e979cd98605} \strng{authornamehash}{6c72ec468af54298a2900e979cd98605} \strng{authorfullhash}{6bdaa983dbe01047e2f444ba195a1273} - \strng{authorfullhashraw}{6bdaa983dbe01047e2f444ba195a1273} \field{sortinit}{L} \field{sortinithash}{7c47d417cecb1f4bd38d1825c427a61a} \field{extradatescope}{labelyear} @@ -1035,7 +788,7 @@ \field{pages}{3246\bibrangedash 3267} \range{pages}{22} \endentry - \entry{Li2022}{article}{}{} + \entry{Li2022}{article}{} \name{author}{4}{ul=2}{% {{un=0,uniquepart=base,hash=32ecf3b8563f881c200eaaf65381ff0d}{% family={Li}, @@ -1064,12 +817,10 @@ } \strng{namehash}{1510ddccc4fc2ac11e1902c1270753e1} \strng{fullhash}{375871951de3a300177779af95d186c2} - \strng{fullhashraw}{375871951de3a300177779af95d186c2} \strng{bibnamehash}{1510ddccc4fc2ac11e1902c1270753e1} \strng{authorbibnamehash}{1510ddccc4fc2ac11e1902c1270753e1} \strng{authornamehash}{1510ddccc4fc2ac11e1902c1270753e1} \strng{authorfullhash}{375871951de3a300177779af95d186c2} - \strng{authorfullhashraw}{375871951de3a300177779af95d186c2} \field{sortinit}{L} \field{sortinithash}{7c47d417cecb1f4bd38d1825c427a61a} \field{extradatescope}{labelyear} @@ -1084,7 +835,7 @@ \field{pages}{7525\bibrangedash 7538} \range{pages}{14} \endentry - \entry{Mills2003}{article}{}{} + \entry{Mills2003}{article}{} \name{author}{8}{}{% {{un=0,uniquepart=base,hash=9962ff894f5d58b58f05b2e31b85302c}{% family={Mills}, @@ -1137,12 +888,10 @@ } \strng{namehash}{80a4e451ce8ba10ca72980e1aa6ed748} \strng{fullhash}{d06e699d7854f71d0511be0899df585f} - \strng{fullhashraw}{d06e699d7854f71d0511be0899df585f} \strng{bibnamehash}{80a4e451ce8ba10ca72980e1aa6ed748} \strng{authorbibnamehash}{80a4e451ce8ba10ca72980e1aa6ed748} \strng{authornamehash}{80a4e451ce8ba10ca72980e1aa6ed748} \strng{authorfullhash}{d06e699d7854f71d0511be0899df585f} - \strng{authorfullhashraw}{d06e699d7854f71d0511be0899df585f} \field{sortinit}{M} \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} \field{extradatescope}{labelyear} @@ -1160,7 +909,7 @@ \verb 10.2527/2003.81123141x \endverb \endentry - \entry{monteny2002b}{article}{}{} + \entry{monteny2002b}{article}{} \name{author}{5}{}{% {{un=0,uniquepart=base,hash=a8bf4cc42c3450651c467edd11d61342}{% family={Monteny}, @@ -1201,12 +950,10 @@ } \strng{namehash}{c6fe4042bee7a26cfb373378d5abbe68} \strng{fullhash}{965e8810c830f4eb2de20abc8875d0ca} - \strng{fullhashraw}{965e8810c830f4eb2de20abc8875d0ca} \strng{bibnamehash}{c6fe4042bee7a26cfb373378d5abbe68} \strng{authorbibnamehash}{c6fe4042bee7a26cfb373378d5abbe68} \strng{authornamehash}{c6fe4042bee7a26cfb373378d5abbe68} \strng{authorfullhash}{965e8810c830f4eb2de20abc8875d0ca} - \strng{authorfullhashraw}{965e8810c830f4eb2de20abc8875d0ca} \field{sortinit}{M} \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} \field{extradatescope}{labelyear} @@ -1225,7 +972,7 @@ \verb 10.3168/jds.S0022-0302(02)74426-3 \endverb \endentry - \entry{nrc2021}{book}{}{} + \entry{nrc2021}{book}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=7712180ec1b113ea720ee1781bc0dfba}{% family={{National Academies of Sciences, Engineering, and Medicine}}, @@ -1239,12 +986,10 @@ } \strng{namehash}{7712180ec1b113ea720ee1781bc0dfba} \strng{fullhash}{7712180ec1b113ea720ee1781bc0dfba} - \strng{fullhashraw}{7712180ec1b113ea720ee1781bc0dfba} \strng{bibnamehash}{7712180ec1b113ea720ee1781bc0dfba} \strng{authorbibnamehash}{7712180ec1b113ea720ee1781bc0dfba} \strng{authornamehash}{7712180ec1b113ea720ee1781bc0dfba} \strng{authorfullhash}{7712180ec1b113ea720ee1781bc0dfba} - \strng{authorfullhashraw}{7712180ec1b113ea720ee1781bc0dfba} \field{sortinit}{N} \field{sortinithash}{22369a73d5f88983a108b63f07f37084} \field{extradatescope}{labelyear} @@ -1254,7 +999,7 @@ \field{title}{Nutrient Requirements of Dairy Cattle: Eighth Revised Edition} \field{year}{2021} \endentry - \entry{nrc2001}{book}{}{} + \entry{nrc2001}{book}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=542dbf807c6825455f75670116436ebd}{% family={{National Research Council}}, @@ -1268,12 +1013,10 @@ } \strng{namehash}{542dbf807c6825455f75670116436ebd} \strng{fullhash}{542dbf807c6825455f75670116436ebd} - \strng{fullhashraw}{542dbf807c6825455f75670116436ebd} \strng{bibnamehash}{542dbf807c6825455f75670116436ebd} \strng{authorbibnamehash}{542dbf807c6825455f75670116436ebd} \strng{authornamehash}{542dbf807c6825455f75670116436ebd} \strng{authorfullhash}{542dbf807c6825455f75670116436ebd} - \strng{authorfullhashraw}{542dbf807c6825455f75670116436ebd} \field{sortinit}{N} \field{sortinithash}{22369a73d5f88983a108b63f07f37084} \field{extradatescope}{labelyear} @@ -1283,7 +1026,7 @@ \field{title}{Nutrient Requirements of Dairy Cattle} \field{year}{2001} \endentry - \entry{nennich2005}{article}{}{} + \entry{nennich2005}{article}{} \name{author}{10}{}{% {{un=0,uniquepart=base,hash=c3738f940594b2a166ffef97684b5ad4}{% family={Nennich}, @@ -1348,12 +1091,10 @@ } \strng{namehash}{38820a0a1acaaa788ddb7d2c0d316d62} \strng{fullhash}{2bdabb61a8d82e9464006f0ea6b2c216} - \strng{fullhashraw}{2bdabb61a8d82e9464006f0ea6b2c216} \strng{bibnamehash}{38820a0a1acaaa788ddb7d2c0d316d62} \strng{authorbibnamehash}{38820a0a1acaaa788ddb7d2c0d316d62} \strng{authornamehash}{38820a0a1acaaa788ddb7d2c0d316d62} \strng{authorfullhash}{2bdabb61a8d82e9464006f0ea6b2c216} - \strng{authorfullhashraw}{2bdabb61a8d82e9464006f0ea6b2c216} \field{sortinit}{N} \field{sortinithash}{22369a73d5f88983a108b63f07f37084} \field{extradatescope}{labelyear} @@ -1372,7 +1113,7 @@ \verb 10.3168/jds.S0022-0302(05)73058-7 \endverb \endentry - \entry{Niu2018}{article}{}{} + \entry{Niu2018}{article}{} \true{moreauthor} \true{morelabelname} \name{author}{3}{}{% @@ -1397,12 +1138,10 @@ } \strng{namehash}{c108249c6c12f1c6e260469e1a89cbd5} \strng{fullhash}{c108249c6c12f1c6e260469e1a89cbd5} - \strng{fullhashraw}{c108249c6c12f1c6e260469e1a89cbd5} \strng{bibnamehash}{c108249c6c12f1c6e260469e1a89cbd5} \strng{authorbibnamehash}{c108249c6c12f1c6e260469e1a89cbd5} \strng{authornamehash}{c108249c6c12f1c6e260469e1a89cbd5} \strng{authorfullhash}{c108249c6c12f1c6e260469e1a89cbd5} - \strng{authorfullhashraw}{c108249c6c12f1c6e260469e1a89cbd5} \field{sortinit}{N} \field{sortinithash}{22369a73d5f88983a108b63f07f37084} \field{extradatescope}{labelyear} @@ -1419,7 +1158,7 @@ \verb 10.1111/gcb.14094 \endverb \endentry - \entry{Pattanaik2003}{article}{}{} + \entry{Pattanaik2003}{article}{} \name{author}{4}{}{% {{un=0,uniquepart=base,hash=6d31146df8b928b65484f1c6bf2bab4e}{% family={Pattanaik}, @@ -1448,12 +1187,10 @@ } \strng{namehash}{1b5cfc06f9b8d19b0060f05f291e7c71} \strng{fullhash}{839623ba0a9c2584ef68eb0b0466a066} - \strng{fullhashraw}{839623ba0a9c2584ef68eb0b0466a066} \strng{bibnamehash}{1b5cfc06f9b8d19b0060f05f291e7c71} \strng{authorbibnamehash}{1b5cfc06f9b8d19b0060f05f291e7c71} \strng{authornamehash}{1b5cfc06f9b8d19b0060f05f291e7c71} \strng{authorfullhash}{839623ba0a9c2584ef68eb0b0466a066} - \strng{authorfullhashraw}{839623ba0a9c2584ef68eb0b0466a066} \field{sortinit}{P} \field{sortinithash}{ff3bcf24f47321b42cb156c2cc8a8422} \field{extradatescope}{labelyear} @@ -1471,7 +1208,7 @@ \verb 10.5713/ajas.2003.1443 \endverb \endentry - \entry{reed2015}{article}{}{} + \entry{reed2015}{article}{} \name{author}{4}{}{% {{un=0,uniquepart=base,hash=7f0a59b8d09ea2d000db2c76aaeb3157}{% family={Reed}, @@ -1500,12 +1237,10 @@ } \strng{namehash}{4ca089edcb03d35b2cd781e1fac91e1d} \strng{fullhash}{934cfbe2369ca76d93c053aa99f2b9ef} - \strng{fullhashraw}{934cfbe2369ca76d93c053aa99f2b9ef} \strng{bibnamehash}{4ca089edcb03d35b2cd781e1fac91e1d} \strng{authorbibnamehash}{4ca089edcb03d35b2cd781e1fac91e1d} \strng{authornamehash}{4ca089edcb03d35b2cd781e1fac91e1d} \strng{authorfullhash}{934cfbe2369ca76d93c053aa99f2b9ef} - \strng{authorfullhashraw}{934cfbe2369ca76d93c053aa99f2b9ef} \field{sortinit}{R} \field{sortinithash}{5e1c39a9d46ffb6bebd8f801023a9486} \field{extradatescope}{labelyear} @@ -1521,7 +1256,7 @@ \field{pages}{3025\bibrangedash 3035} \range{pages}{11} \endentry - \entry{reuven2017}{book}{}{} + \entry{reuven2017}{book}{} \name{author}{2}{}{% {{un=0,uniquepart=base,hash=dcd8140aa0d7fd657829f86e3f5bbddc}{% family={Reuven}, @@ -1542,12 +1277,10 @@ } \strng{namehash}{d83ad99476c9989b7b8cbea5b050d473} \strng{fullhash}{d83ad99476c9989b7b8cbea5b050d473} - \strng{fullhashraw}{d83ad99476c9989b7b8cbea5b050d473} \strng{bibnamehash}{d83ad99476c9989b7b8cbea5b050d473} \strng{authorbibnamehash}{d83ad99476c9989b7b8cbea5b050d473} \strng{authornamehash}{d83ad99476c9989b7b8cbea5b050d473} \strng{authorfullhash}{d83ad99476c9989b7b8cbea5b050d473} - \strng{authorfullhashraw}{d83ad99476c9989b7b8cbea5b050d473} \field{sortinit}{R} \field{sortinithash}{5e1c39a9d46ffb6bebd8f801023a9486} \field{extradatescope}{labelyear} @@ -1557,7 +1290,7 @@ \field{title}{Simulation and the Monte Carlo Method. In: Wiley Series in Probability and Statistics} \field{year}{2017} \endentry - \entry{vadas2007}{article}{}{} + \entry{vadas2007}{article}{} \name{author}{7}{}{% {{un=0,uniquepart=base,hash=0ccd882cd1b35af5e3b66329f8c482b8}{% family={Vadas}, @@ -1604,12 +1337,10 @@ } \strng{namehash}{678003f4d6d3452a1ae65de262babbfd} \strng{fullhash}{07b9400921c16e88e9116e0e416ff058} - \strng{fullhashraw}{07b9400921c16e88e9116e0e416ff058} \strng{bibnamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authorbibnamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authornamehash}{678003f4d6d3452a1ae65de262babbfd} \strng{authorfullhash}{07b9400921c16e88e9116e0e416ff058} - \strng{authorfullhashraw}{07b9400921c16e88e9116e0e416ff058} \field{sortinit}{V} \field{sortinithash}{afb52128e5b4dc4b843768c0113d673b} \field{extradatescope}{labelyear} @@ -1625,7 +1356,7 @@ \field{pages}{324\bibrangedash 332} \range{pages}{9} \endentry - \entry{wilkerson1997prediction}{article}{}{} + \entry{wilkerson1997prediction}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=48edabc88c0262c45263f67866ae9a57}{% family={Wilkerson}, @@ -1648,12 +1379,10 @@ } \strng{namehash}{f20ed2b16b139ef84bf72ff1d9a294a8} \strng{fullhash}{f20ed2b16b139ef84bf72ff1d9a294a8} - \strng{fullhashraw}{f20ed2b16b139ef84bf72ff1d9a294a8} \strng{bibnamehash}{f20ed2b16b139ef84bf72ff1d9a294a8} \strng{authorbibnamehash}{f20ed2b16b139ef84bf72ff1d9a294a8} \strng{authornamehash}{f20ed2b16b139ef84bf72ff1d9a294a8} \strng{authorfullhash}{f20ed2b16b139ef84bf72ff1d9a294a8} - \strng{authorfullhashraw}{f20ed2b16b139ef84bf72ff1d9a294a8} \field{sortinit}{W} \field{sortinithash}{4315d78024d0cea9b57a0c6f0e35ed0d} \field{extradatescope}{labelyear} @@ -1669,7 +1398,7 @@ \field{pages}{3193\bibrangedash 3204} \range{pages}{12} \endentry - \entry{wiltbank2016}{article}{}{} + \entry{wiltbank2016}{article}{} \name{author}{9}{}{% {{un=0,uniquepart=base,hash=a731f4e2eca9c0852b51f0d287e9604d}{% family={Wiltbank}, @@ -1728,12 +1457,10 @@ } \strng{namehash}{c758ac1c173ba36261bd202045a3175c} \strng{fullhash}{4bb2b818929ba010195662fa08ab0440} - \strng{fullhashraw}{4bb2b818929ba010195662fa08ab0440} \strng{bibnamehash}{c758ac1c173ba36261bd202045a3175c} \strng{authorbibnamehash}{c758ac1c173ba36261bd202045a3175c} \strng{authornamehash}{c758ac1c173ba36261bd202045a3175c} \strng{authorfullhash}{4bb2b818929ba010195662fa08ab0440} - \strng{authorfullhashraw}{4bb2b818929ba010195662fa08ab0440} \field{sortinit}{W} \field{sortinithash}{4315d78024d0cea9b57a0c6f0e35ed0d} \field{extradatescope}{labelyear} @@ -1748,7 +1475,7 @@ \field{pages}{239\bibrangedash 253} \range{pages}{15} \endentry - \entry{Wood1967}{article}{}{} + \entry{Wood1967}{article}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=c94c4bde4adfdf61ad0b912763ae5822}{% family={Wood}, @@ -1759,12 +1486,10 @@ } \strng{namehash}{c94c4bde4adfdf61ad0b912763ae5822} \strng{fullhash}{c94c4bde4adfdf61ad0b912763ae5822} - \strng{fullhashraw}{c94c4bde4adfdf61ad0b912763ae5822} \strng{bibnamehash}{c94c4bde4adfdf61ad0b912763ae5822} \strng{authorbibnamehash}{c94c4bde4adfdf61ad0b912763ae5822} \strng{authornamehash}{c94c4bde4adfdf61ad0b912763ae5822} \strng{authorfullhash}{c94c4bde4adfdf61ad0b912763ae5822} - \strng{authorfullhashraw}{c94c4bde4adfdf61ad0b912763ae5822} \field{sortinit}{W} \field{sortinithash}{4315d78024d0cea9b57a0c6f0e35ed0d} \field{extradatescope}{labelyear} @@ -1786,8 +1511,8 @@ \endrefsection \refsection{2} - \datalist[entry]{nyt/global//global/global/global} - \entry{AguirreVillegas2019}{article}{}{} + \datalist[entry]{nyt/global//global/global} + \entry{AguirreVillegas2019}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=c93a22a7a1d4478a5f20770b788f3ae2}{% family={Aguirre-Villegas}, @@ -1810,12 +1535,10 @@ } \strng{namehash}{3f706d7f536fe9b2f2f50ba2001ab49c} \strng{fullhash}{3f706d7f536fe9b2f2f50ba2001ab49c} - \strng{fullhashraw}{3f706d7f536fe9b2f2f50ba2001ab49c} \strng{bibnamehash}{3f706d7f536fe9b2f2f50ba2001ab49c} \strng{authorbibnamehash}{3f706d7f536fe9b2f2f50ba2001ab49c} \strng{authornamehash}{3f706d7f536fe9b2f2f50ba2001ab49c} \strng{authorfullhash}{3f706d7f536fe9b2f2f50ba2001ab49c} - \strng{authorfullhashraw}{3f706d7f536fe9b2f2f50ba2001ab49c} \field{sortinit}{A} \field{sortinithash}{2f401846e2029bad6b3ecc16d50031e2} \field{extradatescope}{labelyear} @@ -1838,7 +1561,7 @@ \verb https://doi.org/10.1016/J.SCITOTENV.2019.134059 \endverb \endentry - \entry{bonifacio2017a}{article}{}{} + \entry{bonifacio2017a}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=2ddb1b41556e6c9ab42634e093b78ae2}{% family={Bonifacio}, @@ -1861,12 +1584,10 @@ } \strng{namehash}{c170dd06eb410415abb1284a01fbb539} \strng{fullhash}{c170dd06eb410415abb1284a01fbb539} - \strng{fullhashraw}{c170dd06eb410415abb1284a01fbb539} \strng{bibnamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authorbibnamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authornamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authorfullhash}{c170dd06eb410415abb1284a01fbb539} - \strng{authorfullhashraw}{c170dd06eb410415abb1284a01fbb539} \field{extraname}{1} \field{sortinit}{B} \field{sortinithash}{d7095fff47cda75ca2589920aae98399} @@ -1883,7 +1604,7 @@ \field{pages}{877\bibrangedash 892} \range{pages}{16} \endentry - \entry{bonifacio2017b}{article}{}{} + \entry{bonifacio2017b}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=2ddb1b41556e6c9ab42634e093b78ae2}{% family={Bonifacio}, @@ -1906,12 +1627,10 @@ } \strng{namehash}{c170dd06eb410415abb1284a01fbb539} \strng{fullhash}{c170dd06eb410415abb1284a01fbb539} - \strng{fullhashraw}{c170dd06eb410415abb1284a01fbb539} \strng{bibnamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authorbibnamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authornamehash}{c170dd06eb410415abb1284a01fbb539} \strng{authorfullhash}{c170dd06eb410415abb1284a01fbb539} - \strng{authorfullhashraw}{c170dd06eb410415abb1284a01fbb539} \field{extraname}{2} \field{sortinit}{B} \field{sortinithash}{d7095fff47cda75ca2589920aae98399} @@ -1928,7 +1647,7 @@ \field{pages}{893\bibrangedash 913} \range{pages}{21} \endentry - \entry{Bucklin2009}{article}{}{} + \entry{Bucklin2009}{article}{} \name{author}{5}{}{% {{un=0,uniquepart=base,hash=1a68f675dfecf59ba940dccd93ca16d7}{% family={Bucklin}, @@ -1963,12 +1682,10 @@ } \strng{namehash}{6927eeaf719db0c9bb4313596e64968a} \strng{fullhash}{1a31d7d711ebf319dd5d576726ce96b7} - \strng{fullhashraw}{1a31d7d711ebf319dd5d576726ce96b7} \strng{bibnamehash}{6927eeaf719db0c9bb4313596e64968a} \strng{authorbibnamehash}{6927eeaf719db0c9bb4313596e64968a} \strng{authornamehash}{6927eeaf719db0c9bb4313596e64968a} \strng{authorfullhash}{1a31d7d711ebf319dd5d576726ce96b7} - \strng{authorfullhashraw}{1a31d7d711ebf319dd5d576726ce96b7} \field{sortinit}{B} \field{sortinithash}{d7095fff47cda75ca2589920aae98399} \field{extradatescope}{labelyear} @@ -1986,7 +1703,7 @@ \verb 10.13031/2013.28851 \endverb \endentry - \entry{Chianese2009a}{article}{}{} + \entry{Chianese2009a}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=8769f8c7f0af5e978c986042db9f7ff7}{% family={Chianese}, @@ -2009,12 +1726,10 @@ } \strng{namehash}{68cb677d5fb3a0ae770e1fab030cc06c} \strng{fullhash}{68cb677d5fb3a0ae770e1fab030cc06c} - \strng{fullhashraw}{68cb677d5fb3a0ae770e1fab030cc06c} \strng{bibnamehash}{68cb677d5fb3a0ae770e1fab030cc06c} \strng{authorbibnamehash}{68cb677d5fb3a0ae770e1fab030cc06c} \strng{authornamehash}{68cb677d5fb3a0ae770e1fab030cc06c} \strng{authorfullhash}{68cb677d5fb3a0ae770e1fab030cc06c} - \strng{authorfullhashraw}{68cb677d5fb3a0ae770e1fab030cc06c} \field{sortinit}{C} \field{sortinithash}{4d103a86280481745c9c897c925753c0} \field{extradatescope}{labelyear} @@ -2035,7 +1750,7 @@ \verb https://elibrary.asabe.org/abstract.asp?aid=27781 \endverb \endentry - \entry{Elsgaard2016}{article}{}{} + \entry{Elsgaard2016}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=3e86451f4170dcfd4cbda91eb02af522}{% family={Elsgaard}, @@ -2058,12 +1773,10 @@ } \strng{namehash}{67ea29a91bc391c16c2a917798549a4f} \strng{fullhash}{67ea29a91bc391c16c2a917798549a4f} - \strng{fullhashraw}{67ea29a91bc391c16c2a917798549a4f} \strng{bibnamehash}{67ea29a91bc391c16c2a917798549a4f} \strng{authorbibnamehash}{67ea29a91bc391c16c2a917798549a4f} \strng{authornamehash}{67ea29a91bc391c16c2a917798549a4f} \strng{authorfullhash}{67ea29a91bc391c16c2a917798549a4f} - \strng{authorfullhashraw}{67ea29a91bc391c16c2a917798549a4f} \field{sortinit}{E} \field{sortinithash}{8da8a182d344d5b9047633dfc0cc9131} \field{extradatescope}{labelyear} @@ -2086,83 +1799,7 @@ \verb https://www.sciencedirect.com/science/article/pii/S0048969715304861 \endverb \endentry - \entry{endres2007behavior}{article}{}{} - \name{author}{2}{}{% - {{un=0,uniquepart=base,hash=9cf4ae31516615ba6a02feacfdcfb638}{% - family={Endres}, - familyi={E\bibinitperiod}, - given={M.\bibnamedelimi I.}, - giveni={M\bibinitperiod\bibinitdelim I\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=bd1e1ceb6a5221e7a4fd7dc42a57ed1d}{% - family={Barberg}, - familyi={B\bibinitperiod}, - given={A.\bibnamedelimi E.}, - giveni={A\bibinitperiod\bibinitdelim E\bibinitperiod}, - givenun=0}}% - } - \strng{namehash}{a53369a049daf687e7189cca489ac1d1} - \strng{fullhash}{a53369a049daf687e7189cca489ac1d1} - \strng{fullhashraw}{a53369a049daf687e7189cca489ac1d1} - \strng{bibnamehash}{a53369a049daf687e7189cca489ac1d1} - \strng{authorbibnamehash}{a53369a049daf687e7189cca489ac1d1} - \strng{authornamehash}{a53369a049daf687e7189cca489ac1d1} - \strng{authorfullhash}{a53369a049daf687e7189cca489ac1d1} - \strng{authorfullhashraw}{a53369a049daf687e7189cca489ac1d1} - \field{sortinit}{E} - \field{sortinithash}{8da8a182d344d5b9047633dfc0cc9131} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Journal of Dairy Science} - \field{title}{Behavior of Dairy Cows in an Alternative Bedded-Pack Housing System} - \field{volume}{90} - \field{year}{2007} - \field{pages}{4192\bibrangedash 4200} - \range{pages}{9} - \endentry - \entry{espejo2007herd}{article}{}{} - \name{author}{2}{}{% - {{un=0,uniquepart=base,hash=486cc8dfdec19691be6c5f7852589615}{% - family={Espejo}, - familyi={E\bibinitperiod}, - given={L.\bibnamedelimi A.}, - giveni={L\bibinitperiod\bibinitdelim A\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=9cf4ae31516615ba6a02feacfdcfb638}{% - family={Endres}, - familyi={E\bibinitperiod}, - given={M.\bibnamedelimi I.}, - giveni={M\bibinitperiod\bibinitdelim I\bibinitperiod}, - givenun=0}}% - } - \strng{namehash}{7bfcb6163318a64575941cca9868ee48} - \strng{fullhash}{7bfcb6163318a64575941cca9868ee48} - \strng{fullhashraw}{7bfcb6163318a64575941cca9868ee48} - \strng{bibnamehash}{7bfcb6163318a64575941cca9868ee48} - \strng{authorbibnamehash}{7bfcb6163318a64575941cca9868ee48} - \strng{authornamehash}{7bfcb6163318a64575941cca9868ee48} - \strng{authorfullhash}{7bfcb6163318a64575941cca9868ee48} - \strng{authorfullhashraw}{7bfcb6163318a64575941cca9868ee48} - \field{sortinit}{E} - \field{sortinithash}{8da8a182d344d5b9047633dfc0cc9131} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Journal of Dairy Science} - \field{number}{1} - \field{title}{Herd-level risk factors for lameness in high-producing Holstein cows housed in freestall barns} - \field{volume}{90} - \field{year}{2007} - \field{pages}{306\bibrangedash 314} - \range{pages}{9} - \verb{doi} - \verb 10.3168/jds.S0022-0302(07)72631-0 - \endverb - \endentry - \entry{Fernandez2015}{article}{}{} + \entry{Fernandez2015}{article}{} \true{moreauthor} \true{morelabelname} \name{author}{6}{}{% @@ -2205,12 +1842,10 @@ } \strng{namehash}{3cdc704cbcf97aeb973f3a6252dabaae} \strng{fullhash}{7dbc06a2c83173d6adaba57acec4a7dc} - \strng{fullhashraw}{7dbc06a2c83173d6adaba57acec4a7dc} \strng{bibnamehash}{3cdc704cbcf97aeb973f3a6252dabaae} \strng{authorbibnamehash}{3cdc704cbcf97aeb973f3a6252dabaae} \strng{authornamehash}{3cdc704cbcf97aeb973f3a6252dabaae} \strng{authorfullhash}{7dbc06a2c83173d6adaba57acec4a7dc} - \strng{authorfullhashraw}{7dbc06a2c83173d6adaba57acec4a7dc} \field{sortinit}{F} \field{sortinithash}{2638baaa20439f1b5a8f80c6c08a13b4} \field{extradatescope}{labelyear} @@ -2233,7 +1868,7 @@ \verb https://doi.org/10.1016/j.watres.2015.06.011 \endverb \endentry - \entry{Fournel2019}{article}{}{} + \entry{Fournel2019}{article}{} \name{author}{5}{}{% {{un=0,uniquepart=base,hash=941092636ab1507f9cab117271622c3d}{% family={Fournel}, @@ -2268,12 +1903,10 @@ } \strng{namehash}{c140d95e5d6d5efc39dbec706a108d79} \strng{fullhash}{6ce811d70a78a8bfd44c05b49af07fee} - \strng{fullhashraw}{6ce811d70a78a8bfd44c05b49af07fee} \strng{bibnamehash}{c140d95e5d6d5efc39dbec706a108d79} \strng{authorbibnamehash}{c140d95e5d6d5efc39dbec706a108d79} \strng{authornamehash}{c140d95e5d6d5efc39dbec706a108d79} \strng{authorfullhash}{6ce811d70a78a8bfd44c05b49af07fee} - \strng{authorfullhashraw}{6ce811d70a78a8bfd44c05b49af07fee} \field{sortinit}{F} \field{sortinithash}{2638baaa20439f1b5a8f80c6c08a13b4} \field{extradatescope}{labelyear} @@ -2290,47 +1923,7 @@ \verb 10.3168/jds.2018-15330 \endverb \endentry - \entry{gomez2010time}{article}{}{} - \name{author}{2}{}{% - {{un=0,uniquepart=base,hash=dcbf59240f81dbaf571a4eb63efb4d1f}{% - family={Gomez}, - familyi={G\bibinitperiod}, - given={A.}, - giveni={A\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=623eff6f91c1b505db03754de9cf2e44}{% - family={Cook}, - familyi={C\bibinitperiod}, - given={N.\bibnamedelimi B.}, - giveni={N\bibinitperiod\bibinitdelim B\bibinitperiod}, - givenun=0}}% - } - \strng{namehash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{fullhash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{fullhashraw}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{bibnamehash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{authorbibnamehash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{authornamehash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{authorfullhash}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \strng{authorfullhashraw}{d0e8f9d3976a803dbf2950d1bc72e4ae} - \field{sortinit}{G} - \field{sortinithash}{32d67eca0634bf53703493fb1090a2e8} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Journal of Dairy Science} - \field{number}{12} - \field{title}{Time budgets of lactating dairy cattle in commercial freestall herds} - \field{volume}{93} - \field{year}{2010} - \field{pages}{5772\bibrangedash 5781} - \range{pages}{10} - \verb{doi} - \verb 10.3168/jds.2010-3436 - \endverb - \endentry - \entry{Hanson2024}{book}{}{} + \entry{Hanson2024}{book}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=35e0ba836b7e802e2dc667e54f37c852}{% family={Hanson}, @@ -2356,12 +1949,10 @@ } \strng{namehash}{bd66932f699665f7f17ec408c0785681} \strng{fullhash}{bd66932f699665f7f17ec408c0785681} - \strng{fullhashraw}{bd66932f699665f7f17ec408c0785681} \strng{bibnamehash}{bd66932f699665f7f17ec408c0785681} \strng{authorbibnamehash}{bd66932f699665f7f17ec408c0785681} \strng{authornamehash}{bd66932f699665f7f17ec408c0785681} \strng{authorfullhash}{bd66932f699665f7f17ec408c0785681} - \strng{authorfullhashraw}{bd66932f699665f7f17ec408c0785681} \field{sortinit}{H} \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} \field{extradatescope}{labelyear} @@ -2372,7 +1963,7 @@ \field{title}{Quantifying Greenhouse Gas Fluxes in Agriculture and Forestry: Methods for Entity-Scale Inventory} \field{year}{2024} \endentry - \entry{Hegg1981}{article}{}{} + \entry{Hegg1981}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=6c0e5d2f176ca8ebeeacf8576d935b35}{% family={Hegg}, @@ -2395,12 +1986,10 @@ } \strng{namehash}{503d1fde573ccccd1d286559fb361049} \strng{fullhash}{503d1fde573ccccd1d286559fb361049} - \strng{fullhashraw}{503d1fde573ccccd1d286559fb361049} \strng{bibnamehash}{503d1fde573ccccd1d286559fb361049} \strng{authorbibnamehash}{503d1fde573ccccd1d286559fb361049} \strng{authornamehash}{503d1fde573ccccd1d286559fb361049} \strng{authorfullhash}{503d1fde573ccccd1d286559fb361049} - \strng{authorfullhashraw}{503d1fde573ccccd1d286559fb361049} \field{sortinit}{H} \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} \field{extradatescope}{labelyear} @@ -2418,7 +2007,7 @@ \verb 10.13031/2013.34204 \endverb \endentry - \entry{IPCC2019}{misc}{}{} + \entry{IPCC2019}{misc}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=92bb724b0d9a20cee031d94d110d683a}{% family={{Intergovernmental Panel on Climate Change}}, @@ -2426,12 +2015,10 @@ } \strng{namehash}{92bb724b0d9a20cee031d94d110d683a} \strng{fullhash}{92bb724b0d9a20cee031d94d110d683a} - \strng{fullhashraw}{92bb724b0d9a20cee031d94d110d683a} \strng{bibnamehash}{92bb724b0d9a20cee031d94d110d683a} \strng{authorbibnamehash}{92bb724b0d9a20cee031d94d110d683a} \strng{authornamehash}{92bb724b0d9a20cee031d94d110d683a} \strng{authorfullhash}{92bb724b0d9a20cee031d94d110d683a} - \strng{authorfullhashraw}{92bb724b0d9a20cee031d94d110d683a} \field{sortinit}{I} \field{sortinithash}{8d291c51ee89b6cd86bf5379f0b151d8} \field{extradatescope}{labelyear} @@ -2448,7 +2035,7 @@ \verb https://www.ipcc-nggip.iges.or.jp/public/2019rf/index.html \endverb \endentry - \entry{IPCC2006}{misc}{}{} + \entry{IPCC2006}{misc}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=676f7b9b8e5bb30500c01e2385e59174}{% family={{IPCC}}, @@ -2456,12 +2043,10 @@ } \strng{namehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{fullhash}{676f7b9b8e5bb30500c01e2385e59174} - \strng{fullhashraw}{676f7b9b8e5bb30500c01e2385e59174} \strng{bibnamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authorbibnamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authornamehash}{676f7b9b8e5bb30500c01e2385e59174} \strng{authorfullhash}{676f7b9b8e5bb30500c01e2385e59174} - \strng{authorfullhashraw}{676f7b9b8e5bb30500c01e2385e59174} \field{sortinit}{I} \field{sortinithash}{8d291c51ee89b6cd86bf5379f0b151d8} \field{extradatescope}{labelyear} @@ -2473,74 +2058,7 @@ \field{title}{Guidelines for National Greenhouse Gas Inventories} \field{year}{2006} \endentry - \entry{jewell2019prevalence}{article}{}{} - \name{author}{7}{}{% - {{un=0,uniquepart=base,hash=768445ba6088f2ec49235eda7e80e5af}{% - family={Jewell}, - familyi={J\bibinitperiod}, - given={M.\bibnamedelimi T.}, - giveni={M\bibinitperiod\bibinitdelim T\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=d691b5968ed6fa3ee172bcfb70ef012f}{% - family={Cameron}, - familyi={C\bibinitperiod}, - given={M.}, - giveni={M\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=b7a5cf8e6ea21cd70352fe6148ca0460}{% - family={Spears}, - familyi={S\bibinitperiod}, - given={J.}, - giveni={J\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=fe6cfa15954be8e6d4e9406b3cda2bf8}{% - family={McKenna}, - familyi={M\bibinitperiod}, - given={S.\bibnamedelimi L.}, - giveni={S\bibinitperiod\bibinitdelim L\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=2b3a623fdd78f96abaccbae1f5994947}{% - family={Cockram}, - familyi={C\bibinitperiod}, - given={M.\bibnamedelimi S.}, - giveni={M\bibinitperiod\bibinitdelim S\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=cd0321bdcd042676b418b7c7b8601974}{% - family={Sanchez}, - familyi={S\bibinitperiod}, - given={J.}, - giveni={J\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=e49ab2aeb81886010134a02fb9a7b3e5}{% - family={Keefe}, - familyi={K\bibinitperiod}, - given={G.\bibnamedelimi P.}, - giveni={G\bibinitperiod\bibinitdelim P\bibinitperiod}, - givenun=0}}% - } - \strng{namehash}{1b414a8e97a6341f002617909898a8a4} - \strng{fullhash}{de50a58a36e916d4c563be4e9b3b9985} - \strng{fullhashraw}{de50a58a36e916d4c563be4e9b3b9985} - \strng{bibnamehash}{1b414a8e97a6341f002617909898a8a4} - \strng{authorbibnamehash}{1b414a8e97a6341f002617909898a8a4} - \strng{authornamehash}{1b414a8e97a6341f002617909898a8a4} - \strng{authorfullhash}{de50a58a36e916d4c563be4e9b3b9985} - \strng{authorfullhashraw}{de50a58a36e916d4c563be4e9b3b9985} - \field{sortinit}{J} - \field{sortinithash}{b2f54a9081ace9966a7cb9413811edb4} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{journaltitle}{Journal of Dairy Science} - \field{number}{4} - \field{title}{Prevalence of lameness and associated risk factors on dairy farms in the Maritime Provinces of Canada} - \field{volume}{102} - \field{year}{2019} - \field{pages}{3392\bibrangedash 3405} - \range{pages}{14} - \endentry - \entry{Jorgensen2009}{article}{}{} + \entry{Jorgensen2009}{article}{} \name{author}{2}{}{% {{un=0,uniquepart=base,hash=ed110bed7af8fb53d47c4c35dc728acd}{% family={Jørgensen}, @@ -2557,12 +2075,10 @@ } \strng{namehash}{3b86e03c39673eb04e57d3c34ec47989} \strng{fullhash}{3b86e03c39673eb04e57d3c34ec47989} - \strng{fullhashraw}{3b86e03c39673eb04e57d3c34ec47989} \strng{bibnamehash}{3b86e03c39673eb04e57d3c34ec47989} \strng{authorbibnamehash}{3b86e03c39673eb04e57d3c34ec47989} \strng{authornamehash}{3b86e03c39673eb04e57d3c34ec47989} \strng{authorfullhash}{3b86e03c39673eb04e57d3c34ec47989} - \strng{authorfullhashraw}{3b86e03c39673eb04e57d3c34ec47989} \field{sortinit}{J} \field{sortinithash}{b2f54a9081ace9966a7cb9413811edb4} \field{extradatescope}{labelyear} @@ -2579,7 +2095,7 @@ \verb 10.1016/j.biortech.2009.01.056 \endverb \endentry - \entry{larney2011}{article}{}{} + \entry{larney2011}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=ccea0a334f0c3e7cc27c859c15a81e76}{% family={Larney}, @@ -2602,12 +2118,10 @@ } \strng{namehash}{50e6caadc107d096bf5458afb07df224} \strng{fullhash}{50e6caadc107d096bf5458afb07df224} - \strng{fullhashraw}{50e6caadc107d096bf5458afb07df224} \strng{bibnamehash}{50e6caadc107d096bf5458afb07df224} \strng{authorbibnamehash}{50e6caadc107d096bf5458afb07df224} \strng{authornamehash}{50e6caadc107d096bf5458afb07df224} \strng{authorfullhash}{50e6caadc107d096bf5458afb07df224} - \strng{authorfullhashraw}{50e6caadc107d096bf5458afb07df224} \field{sortinit}{L} \field{sortinithash}{7c47d417cecb1f4bd38d1825c427a61a} \field{extradatescope}{labelyear} @@ -2624,57 +2138,7 @@ \verb 10.4141/S04-060 \endverb \endentry - \entry{meyer2019contract}{report}{}{} - \name{author}{4}{}{% - {{un=0,uniquepart=base,hash=a5683d1f89988d1a91090b03fd6606d1}{% - family={Meyer}, - familyi={M\bibinitperiod}, - given={D.}, - giveni={D\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=47d2c080e58232ad132bc84baa078318}{% - family={Heguy}, - familyi={H\bibinitperiod}, - given={J.}, - giveni={J\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=8d43abadbd247c36e849a1af146278a4}{% - family={Karle}, - familyi={K\bibinitperiod}, - given={B.}, - giveni={B\bibinitperiod}, - givenun=0}}% - {{un=0,uniquepart=base,hash=123d6dd7d85882c1db2a3bdd8d117515}{% - family={Robinson}, - familyi={R\bibinitperiod}, - given={P.}, - giveni={P\bibinitperiod}, - givenun=0}}% - } - \list{institution}{2}{% - {California Air Resources Board}% - {California Environmental Protection Agency}% - } - \strng{namehash}{1f7b0791713c7cc787ef0bc73f9f46c6} - \strng{fullhash}{47cadaa9366c6edfdf26fdc74df91f3d} - \strng{fullhashraw}{47cadaa9366c6edfdf26fdc74df91f3d} - \strng{bibnamehash}{1f7b0791713c7cc787ef0bc73f9f46c6} - \strng{authorbibnamehash}{1f7b0791713c7cc787ef0bc73f9f46c6} - \strng{authornamehash}{1f7b0791713c7cc787ef0bc73f9f46c6} - \strng{authorfullhash}{47cadaa9366c6edfdf26fdc74df91f3d} - \strng{authorfullhashraw}{47cadaa9366c6edfdf26fdc74df91f3d} - \field{sortinit}{M} - \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{note}{\url{http://ww2.arb.ca.gov/sites/default/files/classic/research/apr/past/16rd002.pdf}} - \field{title}{Contract No. 16RD002} - \field{type}{techreport} - \field{year}{2019} - \endentry - \entry{Mukhtar1999}{report}{}{} + \entry{Mukhtar1999}{report}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=a30e1280a6a0f232d14a729dd02a58dc}{% family={Mukhtar}, @@ -2700,12 +2164,10 @@ } \strng{namehash}{cbdf3154760ef6df370c1f570f9ef0e4} \strng{fullhash}{cbdf3154760ef6df370c1f570f9ef0e4} - \strng{fullhashraw}{cbdf3154760ef6df370c1f570f9ef0e4} \strng{bibnamehash}{cbdf3154760ef6df370c1f570f9ef0e4} \strng{authorbibnamehash}{cbdf3154760ef6df370c1f570f9ef0e4} \strng{authornamehash}{cbdf3154760ef6df370c1f570f9ef0e4} \strng{authorfullhash}{cbdf3154760ef6df370c1f570f9ef0e4} - \strng{authorfullhashraw}{cbdf3154760ef6df370c1f570f9ef0e4} \field{sortinit}{M} \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} \field{extradatescope}{labelyear} @@ -2717,7 +2179,7 @@ \field{type}{techreport} \field{year}{1999} \endentry - \entry{NRCS2017}{misc}{}{} + \entry{NRCS2017}{misc}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=6502d0d6c39ef680aeee2ac35a88c7f5}{% family={{Natural Resources Conservation Service (NRCS)}}, @@ -2725,12 +2187,10 @@ } \strng{namehash}{6502d0d6c39ef680aeee2ac35a88c7f5} \strng{fullhash}{6502d0d6c39ef680aeee2ac35a88c7f5} - \strng{fullhashraw}{6502d0d6c39ef680aeee2ac35a88c7f5} \strng{bibnamehash}{6502d0d6c39ef680aeee2ac35a88c7f5} \strng{authorbibnamehash}{6502d0d6c39ef680aeee2ac35a88c7f5} \strng{authornamehash}{6502d0d6c39ef680aeee2ac35a88c7f5} \strng{authorfullhash}{6502d0d6c39ef680aeee2ac35a88c7f5} - \strng{authorfullhashraw}{6502d0d6c39ef680aeee2ac35a88c7f5} \field{sortinit}{N} \field{sortinithash}{22369a73d5f88983a108b63f07f37084} \field{extradatescope}{labelyear} @@ -2747,7 +2207,7 @@ \verb https://www.nrcs.usda.gov/sites/default/files/2022-10/Waste_Treatment_Lagoon_359_CPS_Oct_2017.pdf \endverb \endentry - \entry{Petersen2024}{article}{}{} + \entry{Petersen2024}{article}{} \name{author}{11}{}{% {{un=0,uniquepart=base,hash=f10952d81d8d2c363347c8fef628b54e}{% family={Petersen}, @@ -2818,12 +2278,10 @@ } \strng{namehash}{aa59ecbf80bce65ec5c8533420f76cf3} \strng{fullhash}{38a8b178a753477dde3d94e4a4f3d67f} - \strng{fullhashraw}{38a8b178a753477dde3d94e4a4f3d67f} \strng{bibnamehash}{aa59ecbf80bce65ec5c8533420f76cf3} \strng{authorbibnamehash}{aa59ecbf80bce65ec5c8533420f76cf3} \strng{authornamehash}{aa59ecbf80bce65ec5c8533420f76cf3} \strng{authorfullhash}{38a8b178a753477dde3d94e4a4f3d67f} - \strng{authorfullhashraw}{38a8b178a753477dde3d94e4a4f3d67f} \field{sortinit}{P} \field{sortinithash}{ff3bcf24f47321b42cb156c2cc8a8422} \field{extradatescope}{labelyear} @@ -2843,7 +2301,7 @@ \verb https://www.sciencedirect.com/science/article/pii/S0301479724002196 \endverb \endentry - \entry{Rotz2023}{report}{}{} + \entry{Rotz2023}{report}{} \name{author}{7}{ul=2}{% {{un=0,uniquepart=base,hash=671322781f92056fc27b16ad1757f430}{% family={Rotz}, @@ -2894,12 +2352,10 @@ } \strng{namehash}{e734e68da4451fe5a5cae09fa18d0e52} \strng{fullhash}{48c257e4237da46f1c6547e3e8901bd1} - \strng{fullhashraw}{48c257e4237da46f1c6547e3e8901bd1} \strng{bibnamehash}{e734e68da4451fe5a5cae09fa18d0e52} \strng{authorbibnamehash}{e734e68da4451fe5a5cae09fa18d0e52} \strng{authornamehash}{e734e68da4451fe5a5cae09fa18d0e52} \strng{authorfullhash}{48c257e4237da46f1c6547e3e8901bd1} - \strng{authorfullhashraw}{48c257e4237da46f1c6547e3e8901bd1} \field{sortinit}{R} \field{sortinithash}{5e1c39a9d46ffb6bebd8f801023a9486} \field{extradatescope}{labelyear} @@ -2910,7 +2366,7 @@ \field{type}{techreport} \field{year}{2023} \endentry - \entry{Rotz2006}{article}{}{} + \entry{Rotz2006}{article}{} \name{author}{2}{}{% {{un=0,uniquepart=base,hash=671322781f92056fc27b16ad1757f430}{% family={Rotz}, @@ -2927,12 +2383,10 @@ } \strng{namehash}{bce699c596f397954035e6ae3aa1d1ca} \strng{fullhash}{bce699c596f397954035e6ae3aa1d1ca} - \strng{fullhashraw}{bce699c596f397954035e6ae3aa1d1ca} \strng{bibnamehash}{bce699c596f397954035e6ae3aa1d1ca} \strng{authorbibnamehash}{bce699c596f397954035e6ae3aa1d1ca} \strng{authornamehash}{bce699c596f397954035e6ae3aa1d1ca} \strng{authorfullhash}{bce699c596f397954035e6ae3aa1d1ca} - \strng{authorfullhashraw}{bce699c596f397954035e6ae3aa1d1ca} \field{sortinit}{R} \field{sortinithash}{5e1c39a9d46ffb6bebd8f801023a9486} \field{extradatescope}{labelyear} @@ -2953,7 +2407,7 @@ \verb https://elibrary.asabe.org/abstract.asp?aid=21731&t=2&redir=&redirType= \endverb \endentry - \entry{Sommer2022}{article}{}{} + \entry{Sommer2022}{article}{} \true{moreauthor} \true{morelabelname} \name{author}{1}{}{% @@ -2966,12 +2420,10 @@ } \strng{namehash}{ee4a7c95e24c930b39421ceaa75e5ffd} \strng{fullhash}{ee4a7c95e24c930b39421ceaa75e5ffd} - \strng{fullhashraw}{ee4a7c95e24c930b39421ceaa75e5ffd} \strng{bibnamehash}{ee4a7c95e24c930b39421ceaa75e5ffd} \strng{authorbibnamehash}{ee4a7c95e24c930b39421ceaa75e5ffd} \strng{authornamehash}{ee4a7c95e24c930b39421ceaa75e5ffd} \strng{authorfullhash}{ee4a7c95e24c930b39421ceaa75e5ffd} - \strng{authorfullhashraw}{ee4a7c95e24c930b39421ceaa75e5ffd} \field{sortinit}{S} \field{sortinithash}{b164b07b29984b41daf1e85279fbc5ab} \field{extradatescope}{labelyear} @@ -2985,7 +2437,7 @@ \field{pages}{41\bibrangedash 55} \range{pages}{15} \endentry - \entry{Sommer2004}{article}{}{} + \entry{Sommer2004}{article}{} \name{author}{3}{}{% {{un=0,uniquepart=base,hash=54e1b143f51177387dff580bea44dd12}{% family={Sommer}, @@ -3008,12 +2460,10 @@ } \strng{namehash}{dc7191ebf5d102792dd701e584ef1d67} \strng{fullhash}{dc7191ebf5d102792dd701e584ef1d67} - \strng{fullhashraw}{dc7191ebf5d102792dd701e584ef1d67} \strng{bibnamehash}{dc7191ebf5d102792dd701e584ef1d67} \strng{authorbibnamehash}{dc7191ebf5d102792dd701e584ef1d67} \strng{authornamehash}{dc7191ebf5d102792dd701e584ef1d67} \strng{authorfullhash}{dc7191ebf5d102792dd701e584ef1d67} - \strng{authorfullhashraw}{dc7191ebf5d102792dd701e584ef1d67} \field{sortinit}{S} \field{sortinithash}{b164b07b29984b41daf1e85279fbc5ab} \field{extradatescope}{labelyear} @@ -3036,7 +2486,7 @@ \verb https://link.springer.com/article/10.1023/b:fres.0000029678.25083.fa \endverb \endentry - \entry{Varma2021}{article}{}{} + \entry{Varma2021}{article}{} \name{author}{7}{}{% {{un=0,uniquepart=base,hash=2977d3dcdc482ea90ed6ada112789899}{% family={Varma}, @@ -3083,12 +2533,10 @@ } \strng{namehash}{b326b50bb8e6e6fc5ee722fdb6772a72} \strng{fullhash}{f67d6f76bc005b4b7f7de13fa7ea0184} - \strng{fullhashraw}{f67d6f76bc005b4b7f7de13fa7ea0184} \strng{bibnamehash}{b326b50bb8e6e6fc5ee722fdb6772a72} \strng{authorbibnamehash}{b326b50bb8e6e6fc5ee722fdb6772a72} \strng{authornamehash}{b326b50bb8e6e6fc5ee722fdb6772a72} \strng{authorfullhash}{f67d6f76bc005b4b7f7de13fa7ea0184} - \strng{authorfullhashraw}{f67d6f76bc005b4b7f7de13fa7ea0184} \field{sortinit}{V} \field{sortinithash}{afb52128e5b4dc4b843768c0113d673b} \field{extradatescope}{labelyear} @@ -3105,45 +2553,18 @@ \verb 10.1016/j.scitotenv.2021.146319 \endverb \endentry - \entry{wallaceDMI}{misc}{}{} - \true{moreauthor} - \true{morelabelname} - \name{author}{1}{}{% - {{un=0,uniquepart=base,hash=d25d7de5091763b498f6461475e2b4ee}{% - family={Wallace}, - familyi={W\bibinitperiod}, - given={Jim}, - giveni={J\bibinitperiod}, - givenun=0}}% - } - \list{institution}{1}{% - {Dairy Management Inc.}% - } - \strng{namehash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{fullhash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{fullhashraw}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{bibnamehash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{authorbibnamehash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{authornamehash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{authorfullhash}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \strng{authorfullhashraw}{5400aff7eb5ccc2fcc51ec2d79a677a1} - \field{sortinit}{W} - \field{sortinithash}{4315d78024d0cea9b57a0c6f0e35ed0d} - \field{extradatescope}{labelyear} - \field{labeldatesource}{} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \field{howpublished}{\url{https://1a2b20e5-7431-4dff-af14-b82106f3ebb5.usrfiles.com/ugd/8aaff4_df19a783dd894a1cbb91ddffc6ab10d5.pdf}} - \field{note}{Accessed: 2023-06-20} - \field{title}{COVERING AND FLARING MANURE STORAGE UNITS AS A POTENTIAL SMALL TO MID-SIZE DAIRY METHANE REDUCTION STRATEGY} - \field{year}{2023} - \endentry \enddatalist + \missing{endres2007behavior} + \missing{espejo2007herd} + \missing{gomez2010time} + \missing{jewell2019prevalence} + \missing{meyer2019contract} + \missing{wallaceDMI} \endrefsection \refsection{4} - \datalist[entry]{nyt/global//global/global/global} - \entry{muck2013recent}{article}{}{} + \datalist[entry]{nyt/global//global/global} + \entry{muck2013recent}{article}{} \name{author}{1}{}{% {{un=0,uniquepart=base,hash=9e97a7f449e0e5f7a53683f931d75eaa}{% family={Muck}, @@ -3154,12 +2575,10 @@ } \strng{namehash}{9e97a7f449e0e5f7a53683f931d75eaa} \strng{fullhash}{9e97a7f449e0e5f7a53683f931d75eaa} - \strng{fullhashraw}{9e97a7f449e0e5f7a53683f931d75eaa} \strng{bibnamehash}{9e97a7f449e0e5f7a53683f931d75eaa} \strng{authorbibnamehash}{9e97a7f449e0e5f7a53683f931d75eaa} \strng{authornamehash}{9e97a7f449e0e5f7a53683f931d75eaa} \strng{authorfullhash}{9e97a7f449e0e5f7a53683f931d75eaa} - \strng{authorfullhashraw}{9e97a7f449e0e5f7a53683f931d75eaa} \field{sortinit}{M} \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} \field{extradatescope}{labelyear} @@ -3177,7 +2596,7 @@ \verb 10.23986/afsci.6718 \endverb \endentry - \entry{pahlow2003microbiology}{incollection}{}{} + \entry{pahlow2003microbiology}{incollection}{} \name{author}{5}{}{% {{un=0,uniquepart=base,hash=55ccb6b3d25b0dc8a39facddef733aa2}{% family={Pahlow}, @@ -3235,16 +2654,13 @@ } \strng{namehash}{88fe406b9e717229845ca2c859347726} \strng{fullhash}{02f4f473c812bbcbbc837bd1e5535856} - \strng{fullhashraw}{02f4f473c812bbcbbc837bd1e5535856} \strng{bibnamehash}{88fe406b9e717229845ca2c859347726} \strng{authorbibnamehash}{88fe406b9e717229845ca2c859347726} \strng{authornamehash}{88fe406b9e717229845ca2c859347726} \strng{authorfullhash}{02f4f473c812bbcbbc837bd1e5535856} - \strng{authorfullhashraw}{02f4f473c812bbcbbc837bd1e5535856} \strng{editorbibnamehash}{fe29230a50af8000d70e73de0812edbc} \strng{editornamehash}{fe29230a50af8000d70e73de0812edbc} \strng{editorfullhash}{fe29230a50af8000d70e73de0812edbc} - \strng{editorfullhashraw}{fe29230a50af8000d70e73de0812edbc} \field{sortinit}{P} \field{sortinithash}{ff3bcf24f47321b42cb156c2cc8a8422} \field{extradatescope}{labelyear} diff --git a/docs/scientific/main.bbl-SAVE-ERROR b/docs/scientific/main.bbl-SAVE-ERROR new file mode 100644 index 0000000000..0cee22bf72 --- /dev/null +++ b/docs/scientific/main.bbl-SAVE-ERROR @@ -0,0 +1,3132 @@ +% $ biblatex auxiliary file $ +% $ biblatex bbl format version 3.2 $ +% Do not modify the above lines! +% +% This is an auxiliary file used by the 'biblatex' package. +% This file may safely be deleted. It will be recreated by +% biber as required. +% +\begingroup +\makeatletter +\@ifundefined{ver@biblatex.sty} + {\@latex@error + {Missing 'biblatex' package} + {The bibliography requires the 'biblatex' package.} + \aftergroup\endinput} + {} +\endgroup + + +\refsection{0} + \datalist[entry]{nyt/global//global/global} + \entry{fan2016root}{article}{} + \name{author}{4}{}{% + {{un=0,uniquepart=base,hash=e15b815678e316512682ce6a40bdf834}{% + family={Fan}, + familyi={F\bibinitperiod}, + given={J.}, + giveni={J\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=71e1badf8f17eed2e3654620cc39ee91}{% + family={McConkey}, + familyi={M\bibinitperiod}, + given={B.}, + giveni={B\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=39856f0439f35f79a8eed8b12d26166c}{% + family={Wang}, + familyi={W\bibinitperiod}, + given={H.}, + giveni={H\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=1253fa8df868f86981529392cea69682}{% + family={Janzen}, + familyi={J\bibinitperiod}, + given={H.}, + giveni={H\bibinitperiod}, + givenun=0}}% + } + \strng{namehash}{32217b75420aafa58aba0cb675133e95} + \strng{fullhash}{d3caf10cab02de4069b53b462bd67037} + \strng{bibnamehash}{32217b75420aafa58aba0cb675133e95} + \strng{authorbibnamehash}{32217b75420aafa58aba0cb675133e95} + \strng{authornamehash}{32217b75420aafa58aba0cb675133e95} + \strng{authorfullhash}{d3caf10cab02de4069b53b462bd67037} + \field{sortinit}{F} + \field{sortinithash}{2638baaa20439f1b5a8f80c6c08a13b4} + \field{extradatescope}{labelyear} + \field{labeldatesource}{} + \field{labelnamesource}{author} + \field{labeltitlesource}{title} + \field{journaltitle}{Field Crops Research} + \field{title}{Root distribution by depth for temperate agricultural crops} + \field{volume}{189} + \field{year}{2016} + \field{pages}{68\bibrangedash 74} + \range{pages}{7} + \verb{doi} + \verb 10.1016/j.fcr.2016.02.013 + \endverb + \verb{urlraw} + \verb https://doi.org/10.1016/j.fcr.2016.02.013 + \endverb + \verb{url} + \verb https://doi.org/10.1016/j.fcr.2016.02.013 + \endverb + \endentry + \entry{hargreaves1985}{article}{} + \name{author}{2}{}{% + {{un=0,uniquepart=base,hash=3a2a388386dde5b212c7bc77ac0322a1}{% + family={Hargreaves}, + familyi={H\bibinitperiod}, + given={George\bibnamedelima H}, + giveni={G\bibinitperiod\bibinitdelim H\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=28a955da7b11477bd50b1497d29c6c65}{% + family={Samani}, + familyi={S\bibinitperiod}, + given={Zohrab\bibnamedelima A}, + giveni={Z\bibinitperiod\bibinitdelim A\bibinitperiod}, + givenun=0}}% + } + \list{publisher}{2}{% + {American Society of Agricultural}% + {Biological Engineers}% + } + \strng{namehash}{6a005ece0e24afb8d7049a7715127ccf} + \strng{fullhash}{6a005ece0e24afb8d7049a7715127ccf} + \strng{bibnamehash}{6a005ece0e24afb8d7049a7715127ccf} + \strng{authorbibnamehash}{6a005ece0e24afb8d7049a7715127ccf} + \strng{authornamehash}{6a005ece0e24afb8d7049a7715127ccf} + \strng{authorfullhash}{6a005ece0e24afb8d7049a7715127ccf} + \field{sortinit}{H} + \field{sortinithash}{23a3aa7c24e56cfa16945d55545109b5} + \field{extradatescope}{labelyear} + \field{labeldatesource}{} + \field{labelnamesource}{author} + \field{labeltitlesource}{title} + \field{journaltitle}{Applied engineering in agriculture} + \field{number}{2} + \field{title}{Reference crop evapotranspiration from temperature} + \field{volume}{1} + \field{year}{1985} + \field{pages}{96\bibrangedash 99} + \range{pages}{4} + \endentry + \entry{hayes2020vindication}{article}{} + \name{author}{2}{}{% + {{un=0,uniquepart=base,hash=5dd552c2d4b881bbc95f627fa9135674}{% + family={Hayes}, + familyi={H\bibinitperiod}, + given={Michael\bibnamedelima HB}, + giveni={M\bibinitperiod\bibinitdelim H\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=d821ecc66c8d49b7cd72446dbe2e0401}{% + family={Swift}, + familyi={S\bibinitperiod}, + given={Roger\bibnamedelima S}, + giveni={R\bibinitperiod\bibinitdelim 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{{un=0,uniquepart=base,hash=d58df4e21e80b2447195fce112543606}{% + family={Parton}, + familyi={P\bibinitperiod}, + given={William\bibnamedelima J}, + giveni={W\bibinitperiod\bibinitdelim J\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=dbfe95e1245daea08d73cf1751adfefd}{% + family={Schimel}, + familyi={S\bibinitperiod}, + given={David\bibnamedelima S}, + giveni={D\bibinitperiod\bibinitdelim S\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=dee55c05f3e8c17c04f1df32a40854f1}{% + family={Cole}, + familyi={C\bibinitperiod}, + given={C\bibnamedelima Vernon}, + giveni={C\bibinitperiod\bibinitdelim V\bibinitperiod}, + givenun=0}}% + {{un=0,uniquepart=base,hash=c54c6a3bfbd13442eeaabc6b36616a35}{% + family={Ojima}, + familyi={O\bibinitperiod}, + given={Dennis\bibnamedelima S}, + giveni={D\bibinitperiod\bibinitdelim S\bibinitperiod}, + givenun=0}}% + } + \list{publisher}{1}{% + {Wiley Online Library}% + } + \strng{namehash}{726d1bbc6906df459be95e0989fbc745} + \strng{fullhash}{ab71d409edd2fafe8a527760d1e5345e} + \strng{bibnamehash}{726d1bbc6906df459be95e0989fbc745} + \strng{authorbibnamehash}{726d1bbc6906df459be95e0989fbc745} + \strng{authornamehash}{726d1bbc6906df459be95e0989fbc745} + \strng{authorfullhash}{ab71d409edd2fafe8a527760d1e5345e} + \field{sortinit}{P} + \field{sortinithash}{ff3bcf24f47321b42cb156c2cc8a8422} + \field{extradatescope}{labelyear} + \field{labeldatesource}{} + \field{labelnamesource}{author} + \field{labeltitlesource}{title} + \field{journaltitle}{Soil Science Society of America Journal} + \field{number}{5} + \field{title}{Analysis of factors controlling soil organic matter levels in Great Plains grasslands} + \field{volume}{51} + \field{year}{1987} + \field{pages}{1173\bibrangedash 1179} + \range{pages}{7} + \endentry + \entry{mu-extsoil}{misc}{} + \name{author}{1}{}{% + {{un=0,uniquepart=base,hash=11d8e6e5fb591c74bd9cd6639f136cb1}{% + family={{University of Missouri Extension}}, + familyi={U\bibinitperiod}}}% + } + \strng{namehash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \strng{fullhash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \strng{bibnamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \strng{authorbibnamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \strng{authornamehash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \strng{authorfullhash}{11d8e6e5fb591c74bd9cd6639f136cb1} + \field{sortinit}{U} + \field{sortinithash}{6901a00e45705986ee5e7ca9fd39adca} + \field{extradatescope}{labelyear} + \field{labeldatesource}{} + \field{labelnamesource}{author} + \field{labeltitlesource}{title} + \field{howpublished}{Publication WQ257, University of Missouri Extension} + \field{note}{Reviewed November 2022; accessed 2023} + \field{title}{Nitrogen in the Environment: Ammonia Volatilization} + \field{year}{2022} + \verb{urlraw} + \verb https://extension.missouri.edu/publications/wq257 + \endverb + \verb{url} + \verb https://extension.missouri.edu/publications/wq257 + \endverb + \endentry + \entry{vadas2007}{article}{} + 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Biber.pm:4678> INFO - Looking for bibtex file 'rufas.bib' for section 1 -[756] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' -[756] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' -[756] Biber.pm:4307> INFO - Sorting list 'nyt/global//global/global/global' of type 'entry' with template 'nyt' and locale 'en-US' -[756] Biber.pm:4313> INFO - No sort tailoring available for locale 'en-US' -[780] Biber.pm:4487> INFO - Processing section 2 -[781] Biber.pm:4678> INFO - Looking for bibtex file 'rufas.bib' for section 2 -[926] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' -[926] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' -[926] Biber.pm:4307> INFO - Sorting list 'nyt/global//global/global/global' of type 'entry' with template 'nyt' and locale 'en-US' -[926] Biber.pm:4313> INFO - No sort tailoring available for locale 'en-US' -[949] Biber.pm:4487> INFO - Processing section 4 -[949] Biber.pm:4678> INFO - Looking for bibtex file 'rufas.bib' for section 4 -[988] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' -[988] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' -[988] Biber.pm:4307> INFO - Sorting list 'nyt/global//global/global/global' of type 'entry' with template 'nyt' and locale 'en-US' -[988] Biber.pm:4313> INFO - No sort tailoring available for locale 'en-US' -[990] bbl.pm:676> INFO - Writing 'main.bbl' with encoding 'UTF-8' -[1033] bbl.pm:779> INFO - Output to main.bbl +[0] Config.pm:307> INFO - This is Biber 2.19 +[0] Config.pm:310> INFO - Logfile is 'main.blg' +[135] biber-MSWIN64:340> INFO - === +[180] Biber.pm:419> INFO - Reading 'main.bcf' +[329] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[332] Biber.pm:979> INFO - Found 29 citekeys in bib section 1 +[332] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[335] Biber.pm:979> INFO - Found 28 citekeys in bib section 2 +[336] Biber.pm:979> INFO - Found 6 citekeys in bib section 0 +[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 3 +[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[336] Biber.pm:979> INFO - Found 2 citekeys in bib section 4 +[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[376] Biber.pm:4419> INFO - Processing section 0 +[391] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 0 +[442] bibtex.pm:1713> INFO - LaTeX decoding ... +[524] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib' +[572] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[572] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[572] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[572] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[574] Biber.pm:4419> INFO - Processing section 1 +[574] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1 +[792] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[792] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[792] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[792] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[837] Biber.pm:4419> INFO - Processing section 2 +[838] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 2 +[1031] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[1031] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[1031] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[1031] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[1066] Biber.pm:4419> INFO - Processing section 4 +[1067] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 4 +[1119] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[1119] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[1119] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[1119] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[1122] bbl.pm:660> INFO - Writing 'main.bbl' with encoding 'UTF-8' +[1183] bbl.pm:763> INFO - Output to main.bbl +[1185] Biber.pm:131> WARN - I didn't find a database entry for 'hargreaves1985' (section 0) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'mu-extsoil' (section 0) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'hayes2020vindication' (section 0) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'parton1987analysis' (section 0) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'fan2016root' (section 0) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'gomez2010time' (section 2) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'espejo2007herd' (section 2) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'jewell2019prevalence' (section 2) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'meyer2019contract' (section 2) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'endres2007behavior' (section 2) +[1186] Biber.pm:131> WARN - I didn't find a database entry for 'wallaceDMI' (section 2) +[1186] Biber.pm:133> INFO - WARNINGS: 11 diff --git a/docs/scientific/main.fdb_latexmk b/docs/scientific/main.fdb_latexmk index 6a384bcb9f..c594b67914 100644 --- a/docs/scientific/main.fdb_latexmk +++ b/docs/scientific/main.fdb_latexmk @@ -1,301 +1,323 @@ # Fdb version 4 -["biber main"] 1770301617.46208 "main.bcf" "main.bbl" "main" 1770301634.9945 0 - "main.bcf" 1770301634 121765 591e589255f4b16f258226ea663b8582 "pdflatex" - "rufas.bib" 1770235169 25022 cd052fc63428d6a4873c3689db3e71ac "" +["biber main"] 1773836238.10959 "main.bcf" "main.bbl" "main" 1773836265.77658 0 + "main.bcf" 1773836264 120814 10a9c52fee9bb7676941633b64307201 "pdflatex" + "resources/animal.bib" 1773235466 19843 003ce6dc3163a9c1fd885dbc082d404e "" (generated) "main.bbl" "main.blg" (rewritten before read) -["pdflatex"] 1770301627.4456 "c:/Users/Kristan 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-\contentsline {figure}{\numberline {2}{\ignorespaces This is a high level schematic to illustrate the methodology behind the heifer breeding and re-breeding in RuFaS Animal Module.}}{70}{figure.caption.7}% -\contentsline {figure}{\numberline {3}{\ignorespaces This is a high level schematic to illustrate the methodology behind the cow breeding and re-breeding in RuFaS Animal Module.}}{72}{figure.caption.8}% -\contentsline {figure}{\numberline {4}{\ignorespaces A schematic illustrating the flow of milk reduction in ration formulation logic.}}{83}{figure.caption.9}% -\babel@toc {english}{}\relax -\contentsline {figure}{\numberline {5}{\ignorespaces A real-world example of a simplistic manure management chain. }}{9}{figure.caption.12}% -\contentsline {figure}{\numberline {6}{\ignorespaces The manure management chain illustrated in the previous figure, with RuFaS-specific information reflected. }}{9}{figure.caption.13}% -\contentsline {figure}{\numberline {7}{\ignorespaces If manure from a pen is routed to two different general manure streams, two sets of manure stream inputs must be defined. An example of a single pen’s manure stream inputs is above - in this example, manure from this pen is routed to two locations, one representing an exercise lot, the other representing a bedded pack area.}}{15}{figure.caption.15}% -\contentsline {figure}{\numberline {8}{\ignorespaces \relax }}{96}{figure.caption.45}% -\contentsline {figure}{\numberline {9}{\ignorespaces Example of the metadata input file.}}{9}{figure.caption.46}% -\contentsline {figure}{\numberline {10}{\ignorespaces Farm grown feed allocation to cattle groups }}{8}{figure.caption.48}% diff --git a/docs/scientific/main.lot b/docs/scientific/main.lot deleted file mode 100644 index 4f51583837..0000000000 --- a/docs/scientific/main.lot +++ /dev/null @@ -1,96 +0,0 @@ -\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{11}{table.1}% -\contentsline {table}{\numberline {2}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section}}{12}{table.2}% -\contentsline {table}{\numberline {3}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section.}}{12}{table.3}% -\contentsline {table}{\numberline {4}{\ignorespaces The user must define at least 3 pens and for each pen, key inputs are:}}{16}{table.4}% -\contentsline {table}{\numberline {6}{\ignorespaces A summary of animal types}}{17}{table.caption.2}% -\contentsline {table}{\numberline {7}{\ignorespaces Key variables used in protein requirement calculations.}}{24}{table.7}% -\contentsline {table}{\numberline {8}{\ignorespaces Key variables used in mineral requirement calculations.}}{27}{table.8}% -\contentsline {table}{\numberline {9}{\ignorespaces Key variables used in DMI requirement calculations.}}{28}{table.9}% -\contentsline {table}{\numberline {10}{\ignorespaces Key variables used in protein requirement calculations.}}{34}{table.10}% -\contentsline {table}{\numberline {11}{\ignorespaces Key variables used in mineral requirement calculations.}}{37}{table.11}% -\contentsline {table}{\numberline {12}{\ignorespaces Key variables used in DMI estimation calculations.}}{39}{table.12}% -\contentsline {table}{\numberline {13}{\ignorespaces Essential and non-essential amino acids}}{39}{table.13}% -\contentsline {table}{\numberline {14}{\ignorespaces Key variables used in calculation of AA.}}{41}{table.14}% -\contentsline {table}{\numberline {15}{\ignorespaces Key variables used in calculation of net energy in NRC 2001.}}{45}{table.15}% -\contentsline {table}{\numberline {16}{\ignorespaces Key variables used in calculation of net energy supply from NASEM 2021.}}{47}{table.16}% -\contentsline {table}{\numberline {17}{\ignorespaces Key variables used in calculation of AA.}}{50}{table.17}% -\contentsline {table}{\numberline {18}{\ignorespaces Key variables used in calculation of AA.}}{50}{table.18}% -\contentsline {table}{\numberline {19}{\ignorespaces Key inputs found in the animal input file.}}{53}{table.19}% -\contentsline {table}{\numberline {20}{\ignorespaces Key inputs found in the feed input file.}}{54}{table.20}% -\contentsline {table}{\numberline {21}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{55}{table.21}% -\contentsline {table}{\numberline {22}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{56}{table.22}% -\contentsline {table}{\numberline {23}{\ignorespaces Below is a summary of the user inputs that are available and their definitions.}}{61}{table.23}% -\contentsline {table}{\numberline {24}{\ignorespaces Below are the key user inputs that determine the \textbf {heifer reproductive breeding program} and impact reproductive efficiency and age at first calving.}}{66}{table.caption.5}% -\contentsline {table}{\numberline {25}{\ignorespaces The following inputs determine reproductive efficiency of cows and influence culling, calving interval, and calf output.}}{67}{table.25}% -\contentsline {table}{\numberline {26}{\ignorespaces The following inputs can be used to determine if there is a \textbf {decrease in the conception rate} with parity and rebreeding attempts.}}{68}{table.caption.6}% -\contentsline {table}{\numberline {27}{\ignorespaces Important functions for the reproduction section.}}{74}{table.27}% -\contentsline {table}{\numberline {28}{\ignorespaces The following user inputs are used to estimate customized herd-level lactation curve parameters. See the Methodology section of this document and the Lactation Curve Scientific Documentation for more detail about how these inputs are used with relation to daily milk production.}}{77}{table.28}% -\contentsline {table}{\numberline {29}{\ignorespaces The following inputs are used to determine the milk fat and milk protein percentages for each lactating cow}}{78}{table.29}% -\contentsline {table}{\numberline {30}{\ignorespaces The following inputs are used to constrain how much an average cow’s daily milk production will be reduced due to an inadequate ration. See the Methodology section of this document and the Ration Formulation scientific documentation for more detail about how these inputs are used with relation to daily milk production.}}{79}{table.30}% -\contentsline {table}{\numberline {31}{\ignorespaces Wood's Lactation Curve Base Parameters – These inputs provide the baseline values and variability for Wood’s lactation curve parameters as derived from \blx@tocontentsinit {1}\textcite {Li2022}.}}{85}{table.31}% -\contentsline {table}{\numberline {33}{\ignorespaces Adjustment Factors – These factors adjust the base parameters based on geographical, temporal, management, and parity considerations.}}{86}{table.33}% -\contentsline {table}{\numberline {35}{\ignorespaces Farm Specific 305-Day Milk Production — These inputs help tailor the lactation curve to the farm’s production targets and herd composition.}}{87}{table.35}% -\contentsline {table}{\numberline {36}{\ignorespaces Summary of important functions for the reproduction section. }}{88}{table.36}% -\contentsline {table}{\numberline {37}{\ignorespaces The following inputs are used to determine the probability and timing of cow death and sales events.}}{92}{table.37}% -\contentsline {table}{\numberline {38}{\ignorespaces Cumulative distribution function (CDF) values associated with the conditional probability that a sold animal is removed due to each group of issues and/or the conditional probability of death over time. Corresponds to the “probability” value for each cull reason in the animal input json file. The 'cull\_day\_count' array defines the segments of the CDF}}{97}{table.caption.10}% -\contentsline {table}{\numberline {39}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{99}{table.39}% -\contentsline {table}{\numberline {40}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{99}{table.40}% -\contentsline {table}{\numberline {41}{\ignorespaces These inputs define phosphorus-related outputs relevant to lactating cows.}}{100}{table.41}% -\contentsline {table}{\numberline {42}{\ignorespaces Expected outputs from this section.}}{100}{table.42}% -\contentsline {table}{\numberline {43}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{110}{table.43}% -\contentsline {table}{\numberline {44}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{110}{table.44}% -\contentsline {table}{\numberline {45}{\ignorespaces Inputs specific to the methane emissions model and selected mitigation strategies.}}{111}{table.45}% -\contentsline {table}{\numberline {46}{\ignorespaces Expected outputs from this section.}}{111}{table.46}% -\contentsline {table}{\numberline {47}{\ignorespaces General dietary fiber and fat concentration inputs.}}{114}{table.47}% -\contentsline {table}{\numberline {48}{\ignorespaces Feed-based methane mitigation strategies.}}{114}{table.48}% -\contentsline {table}{\numberline {49}{\ignorespaces Dosage of methane mitigation additives.}}{114}{table.49}% -\contentsline {table}{\numberline {50}{\ignorespaces Expected outputs from this section.}}{114}{table.50}% -\contentsline {table}{\numberline {51}{\ignorespaces Common abbreviations used throughout this document}}{116}{table.51}% -\babel@toc {english}{}\relax -\contentsline {table}{\numberline {52}{\ignorespaces Examples of processor types by class.}}{8}{table.caption.11}% -\contentsline {table}{\numberline {53}{\ignorespaces List of Python classes for Animal to Manure Module connection.}}{11}{table.caption.14}% -\contentsline {table}{\numberline {54}{\ignorespaces User inputs for Stream Formation and Bedding sections.}}{12}{table.54}% -\contentsline {table}{\numberline {55}{\ignorespaces Recommended minutes\_away\_for\_milking by pen type based on published literature. Remember, this does not necessarily reflect the model defaults. }}{17}{table.caption.16}% -\contentsline {table}{\numberline {56}{\ignorespaces Proportions of differnt streams for different animal classes.}}{17}{table.caption.17}% -\contentsline {table}{\numberline {57}{\ignorespaces Calculated manure and bedding characteristics}}{19}{table.caption.18}% -\contentsline {table}{\numberline {58}{\ignorespaces The classes of handlers that are used in this module.}}{21}{table.caption.19}% -\contentsline {table}{\numberline {59}{\ignorespaces Required inputs for the Manure Handler (refreshed\_manure\_management.json)}}{21}{table.caption.20}% -\contentsline {table}{\numberline {60}{\ignorespaces The surface area per stall that is covered with manure is a function of the pen type and type of animal housed.}}{24}{table.caption.21}% -\contentsline {table}{\numberline {61}{\ignorespaces Calculated manure storage variables and their units}}{28}{table.caption.22}% -\contentsline {table}{\numberline 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based on presence or absence of mixing and average annual air temperature.}}{66}{table.caption.34}% -\contentsline {table}{\numberline {78}{\ignorespaces Calculated manure storage variables and their units}}{72}{table.78}% -\contentsline {table}{\numberline {79}{\ignorespaces Classes available in open lots.}}{75}{table.caption.35}% -\contentsline {table}{\numberline {80}{\ignorespaces Required inputs for the open lots section}}{75}{table.caption.36}% -\contentsline {table}{\numberline {81}{\ignorespaces Calculated manure storage variables and their units}}{82}{table.81}% -\contentsline {table}{\numberline {82}{\ignorespaces Classes available in composting.}}{84}{table.caption.37}% -\contentsline {table}{\numberline {83}{\ignorespaces Required inputs for the composting section (refreshed\_manure\_management.json)}}{85}{table.caption.38}% -\contentsline {table}{\numberline {84}{\ignorespaces Methane conversion factor values for compost pens, based on composting method and average annual air temperature.}}{86}{table.caption.39}% -\contentsline {table}{\numberline {85}{\ignorespaces NH\textsubscript {3}-N emission factors for compost by composting method.}}{90}{table.caption.40}% -\contentsline {table}{\numberline {86}{\ignorespaces N\textsubscript {2}O-N emission factors for compost by composting method.}}{91}{table.caption.42}% -\contentsline {table}{\numberline {87}{\ignorespaces Manure storage variable calculations}}{92}{table.87}% -\contentsline {table}{\numberline {88}{\ignorespaces List of classes for daily spread.}}{93}{table.caption.43}% -\contentsline {table}{\numberline {89}{\ignorespaces Required inputs for the daily spread section (refreshed\_manure\_management.json)}}{93}{table.caption.44}% -\contentsline {table}{\numberline {90}{\ignorespaces The key constants for all equations in the Manure Module}}{98}{table.90}% -\contentsline {table}{\numberline {91}{\ignorespaces Common abbreviations used throughout this document}}{100}{table.91}% -\contentsline 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\rule{\textwidth}{1pt} -} - -\renewcommand{\footrulewidth}{0.4pt} -\fancyfoot[L]{% - \begin{tabular}[t]{@{}l@{}} - Ruminant Farm System\\ - Sci Doc v.1 - \end{tabular}% -} -\fancyfoot[C]{\thepage} -\fancyfoot[R]{% - \begin{tabular}[t]{@{}r@{}} - \nouppercase{\leftmark}\\ - \end{tabular}% -} -\fancypagestyle{landscapeplain}{ - \fancyhf{} - \renewcommand{\headrulewidth}{0pt} - \renewcommand{\footrulewidth}{0pt} -} - -% Bibliography setup -\usepackage[ - backend=biber, - style=authoryear, - natbib=true -]{biblatex} - -\addbibresource{rufas.bib} - -\usepackage{titlesec} -\usepackage{etoolbox} - -% Reset subsection counter at each new section -\pretocmd{\section}{\setcounter{subsection}{0}}{}{} - -% Roman for \section, Alpha for \subsection, alpha for \subsubsection -\renewcommand{\thesection}{\Roman{section}.} -\renewcommand{\thesubsection}{\Alph{subsection}.} -\renewcommand{\thesubsubsection}{\alph{subsubsection}.} - -% --- Title Formats (in size order) --- -\titleformat{\section} - {\Large\bfseries} - {\thesection} - {1em} - {} - -\titleformat{\subsection} - {\normalsize\bfseries} - {\thesubsection} - {1em} - {} - -\titleformat{\subsubsection} - {\normalsize\bfseries} - {\thesubsubsection} - {1em} - {} - -% --- Spacing for each level --- -\titlespacing*{\section}{0pt}{1.5\baselineskip}{1\baselineskip} -\titlespacing*{\subsection}{0pt}{1\baselineskip}{0.5\baselineskip} -\titlespacing*{\subsubsection}{0pt}{0.75\baselineskip}{0.35\baselineskip} +\input{preamble} \begin{document} +% Custom Title Page +\begin{titlepage} + \thispagestyle{empty} + \centering + \vspace*{2cm} + + {\Huge\bfseries Ruminant Farm System Model\par} + {\Huge\bfseries (RuFaS)\par} + \vspace{0.5cm} + + {\Large Scientific Documentation\par} + \vspace{1cm} + + + + \includegraphics[width=1\textwidth]{resources/rufastitlepgimg.png} % Adjust size and filename + \vspace{1cm} + \vfill + + {\small v.1; Updated \today\par} + \vspace*{1cm} +\end{titlepage} +\newpage + + +\setcounter{tocdepth}{2} % includes \part (-1) and \section (1), excludes \subsection (2+) +\tableofcontents +\clearpage + +% --- Preface --- +\part{Preface: A Day in the Life on a RuFaS Farm}\label{rufasday} + +This document provides a high-level overview of the daily operations of a ruminant farm, as modeled by RuFaS. The overview will be through the eyes of Dr. Rue Fas. One day, Dr. Rue woke up and decided the life of a computer scientist wasn’t for her. So she bought a dairy farm, and this is how she operates it every day. + +\paragraph{Feeding the Animals} +Second thing in the morning, after coffee, Dr. Rue checks the calendar to see if it’s time to formulate a new ration for her animals. +\vspace{0.2cm} + +If a new ration needs to be formulated, Dr. Rue heads over to the barn where she keeps all her forages and feed. While there, she checks how well all the forages are holding up. After considering the feeds available, the quality of each one, and how much each one costs, she decides on how productive she wants her animals to be. It is a difficult balancing act, but eventually a ration recipe is found that will keep the animals happy while keeping costs low and sustainability high until the calendar says the ration recipe needs to be reformulated. +\vspace{0.2cm} + +When Dr. Rue doesn’t need to formulate a new ration, she takes the last ration recipe she made and grabs all the feed and forage the animals need for the day out of the feed barn. If there isn’t enough for the animals, then a new ration is formulated using the steps above. + +\paragraph{Taking Care of the Animals} +After making sure all the animals’ feed is taken care of, Dr. Rue moves on to taking care of all the other animal tasks. This includes milking the animals, making sure they’re healthy, getting them pregnant, and numerous other tasks. +\vspace{0.2cm} + +As dawn breaks on the RuFaS farm, the animals awaken after a restful night. Joe, the farm master, prepares a large whiteboard to track HerdReproductionStatistics, ensuring he has all the data he needs for the day’s activities. + +\textit{Daily Routine} - After leaving their pens, each animal lines up in front of the barn. Julie, the diligent farm veterinarian, examines them one by one. This daily check includes updates on the following areas: +\begin{itemize} + \item Nutrients: Each animal begins its day with a quick phosphorus requirement assessment. Julie records these details and updates the animal’s phosphorus-related metrics. + \item Digestive System: With nutrient information in hand, Julie shifts focus to each animal’s digestive system, estimating manure output and enteric methane production for that day. + + \item Milk Production: All milking cows are assessed to gauge daily milk yield and milk component content (fat and protein). Any necessary adjustments are noted. + + \item Animal Growth: Around midday, Julie returns to each animal to evaluate daily weight changes. She updates each animal’s body weight accordingly. + + \item Reproduction: HeiferII and Cow stage animals undergo a reproduction check. Julie closely monitors their reproductive progress and updates the HerdReproductionStatistics details on Joe’s whiteboard. + + \item Life Stage Evaluation: Once the daily routines are complete, Julie determines if any animal is ready to progress to the next life stage. Graduating animals are marked as “graduated” to be moved to their new pens. Animals that must leave the herd—due to health, productivity, or other issues—are labeled as “sold” or “dead” to be removed from the farm population. + + \item Herd Size Maintenance: After every animal has been evaluated, Joe counts the herd to ensure it remains at a healthy size. If it is too large, he arranges the sale of some animals. If the herd is too small, he may opt to purchase additional heiferIIIs to keep numbers at the ideal level. + + \item Herd Structure Management: Joe also manages pen assignments. Newly graduated or newborn animals are guided to suitable pens, while animals marked for removal (sold or deceased) are taken out of the herd and removed from the farm records. +\end{itemize} + + +\textit{Output Reporting} +At day’s end, Joe and Julie review the updated HerdReproductionStatistics on the whiteboard. Joe then compiles a concise report summarizing the day’s herd stats. He forwards this information to the OutputManager before wrapping up another successful day on the RuFaS farm. +\vspace{0.5cm} + +\paragraph{Dealing with the Manure} +Once all the animal chores are finished, Dr. Rue moves on to handling the manure. There are a lot of different ways that manure is collected from the animals: it is flushed out of the milking parlor with water, some of the pens need to have it shoveled out along with the bedding in the pen, and some pens have grates that allow the manure to go straight into a pit beneath the barn. +\vspace{0.2cm} + +There are a lot of different places where manure is processed and stored on the farm. Dr. Rue goes from place to place on the farm, moving the manure from one place to the next. The manure chores are finished after moving all of the manure into her lagoons, compost piles, and other storages. As this final manure chore is completed, she writes down all the information about how much manure is in all these storages, and some information about what that manure is made of. How much water, nitrogen, phosphorus, other solids, etc. are in each storage. + +\paragraph{Managing the Fields} +Now that Dr. Rue is done making sure all the manure has been handled and stored properly, she can take care of all the field tasks. She has a lot of fields on her farm, each with its own unique schedule. Her field management routine starts with checking each field’s schedule to see if any of them are due to have manure applied, and if so, how much they should have applied. After noting all the manure that is supposed to go onto her fields, these amounts are checked against the amounts of manure that are in her manure storage. Dr. Rue then applies manure to each field on the schedule that day, trying to match the amount applied to the amount on the schedule as best she can. +\vspace{0.2cm} + +After making sure every manure item on each farm’s schedule has been taken care of for the day, the schedule for each field is rechecked, one field at a time. In each schedule she checks to see if that field needs to be tilled, if any chemical fertilizer needs to be applied, and if any crops need to be planted or harvested. After all these activities are taken care of, Mother Nature goes to work. The sun shines and rain falls, providing the field with water and energy that grows crops and soaks the soil. After taking care of each field one by one, Dr. Rue drives back to the main farm with all of the crops that she harvested on that day. + +\paragraph{Storing the Feeds} +Now that she is back at the barns, all the crops that were just harvested can be stored. Fortunately she is very organized, so all her harvested crops are separate from one another and each has a label, indicating where it will be stored inside the feed barn. As each feed is stored, it is labeled with the current date. Dr. Rue is exhausted from another long day. She goes back to the farmhouse and rests up, preparing to do the whole thing over again tomorrow. Her daily routine might seem repetitive, but each day is a crucial part of the larger, continuous process that keeps her farm running efficiently and sustainably. + + + +\newpage \include{animal} \include{manure} \include{crop_and_soil} \include{feed_storage} + +\newpage +\part{Abbreviations} + +\renewcommand{\arraystretch}{1.3} +\newcolumntype{L}[1]{>{\RaggedRight\arraybackslash}p{#1}} + +% optionally tighten column padding just for this table +\setlength{\tabcolsep}{4pt} + +\begin{longtable}{@{} L{0.23\textwidth} L{0.70\textwidth} @{}} % 0.93*textwidth + padding < textwidth +\caption{Common abbreviations used throughout this document} \\ + +\toprule +\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ +\midrule +\endfirsthead + +\multicolumn{2}{@{}l}{\textit{Table continued from previous page}} \\ +\toprule +\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ +\midrule +\endhead + +\midrule +\multicolumn{2}{@{}r@{}}{\textit{Continued on next page}} \\ +\endfoot + +\bottomrule +\endlastfoot + +ADF & Acid detergent fiber (\% of DM) \\ +ADG & Average daily weight gain (g/d) \\ +Age1stBred & First breeding age (month) \\ +BCS5 & Body condition score (1–5 basis) \\ +BW & Body weight (kg) \\ +Ca & Calcium content (\% of DM) \\ +CBW & Calf birth weight (kg) \\ +CI & Calving interval (d) \\ +cm & centimeter \\ +Cost & Feed cost (\$/kg of DM) \\ +CP & Crude protein (\% of DM) \\ +d & days \\ +DE & Digestible energy (standard value, Mcal/kg) \\ +DIM & Days in milk \\ +DM & Dry matter (\% of as-fed basis) \\ +DMI & Dry matter intake \\ +DOP & Days of pregnancy (d) \\ +dRUP & RUP degradability (\% of RUP) \\ +EE & Ether extract, in crude fat (\% DM) \\ +EndCP & Endogenous CP \\ +EndN & Endogenous N \\ +EQSBW & Equivalent shrunk body weight (kg) \\ +FA & Fatty acids \\ +FIPS & Federal Information Processing Standards \\ +g & grams \\ +GE & Gross energy (standard value, Mcal/kg) \\ +GrUterW & Gravid uterine weight (kg) \\ +Kd & Rumen protein degradation rate (\%/h) \\ +kg & kilograms \\ +kJ & kilojoule \\ +L & liters \\ +m & meter \\ +max & maximum \\ +Mcal & Megacalorie \\ +MCP & Microbial Crude Protein \\ +ME & Metabolizable energy (standard value, Mcal/kg) \\ +MICP & Microbial CP \\ +min & minimum \\ +mL & milliliters \\ +MN & Microbial N \\ +MP & Metabolizable protein \\ +MTP & Microbial TP \\ +MW & Mature body weight (kg) \\ +MY & Milk yield \\ +N & Nitrogen (\% of DM) \\ +NASEM & National Academies of Sciences, Engineering, and Medicine \\ +NDF & Neutral detergent fiber (\% of DM) \\ +NEG & Net energy for growth (standard value, Mcal/kg) \\ +NEL & Net energy for lactation (standard value, Mcal/kg) \\ +NEM & Net energy for maintenance (standard value, Mcal/kg) \\ +nNDF & Nondigestible Neutral Detergent Fiber \\ +NPN & Non-protein Nitrogen \\ +NRC & National Research Council (updated in 2021 to NASEM) \\ +OM & Organic matter (\% of DM) \\ +P & Phosphorus content (\% of DM) \\ +PAF & Processing adjustment factor (not used) \\ +Parity & Number of lactations \\ +PrevTemp & Average daily temperature of last month (°C) \\ +RDP & Ruminally degraded CP \\ +ROM & Residual OM (\% of DM) \\ +RUP & Ruminally undegraded CP \\ +s & seconds \\ +TAN & Total ammoniacal N \\ +TDN & Total digestible nutrient (\% of DM) \\ +TP & True protein (\% of DM) \\ +USDA & United States Department of Agriculture \\ +UterW & Uterine weight (kg) \\ +WSC & Water Soluble Carbohydrates \\ +\end{longtable} + \end{document} diff --git a/docs/scientific/main.toc b/docs/scientific/main.toc index 50fcdc305f..63453b835a 100644 --- a/docs/scientific/main.toc +++ b/docs/scientific/main.toc @@ -1,245 +1,343 @@ -\contentsline {section}{\numberline {I.}Preface: A Day in the Life on a RuFaS Farm}{8}{section.1}% -\contentsline {paragraph}{Feeding the Animals}{8}{section.1}% -\contentsline {paragraph}{Taking Care of the Animals}{8}{section.1}% -\contentsline {paragraph}{Dealing with the Manure}{9}{section.1}% -\contentsline {paragraph}{Managing the Fields}{9}{section.1}% -\contentsline {paragraph}{Storing the Feeds}{9}{section.1}% -\contentsline {section}{\numberline {II.}Module Introduction}{9}{section.2}% -\contentsline {subsection}{\numberline {A.}Animal Life Cycle}{10}{subsection.2.1}% -\contentsline {section}{\numberline {III.}Herd-level Processes and Management}{11}{section.3}% -\contentsline {subsection}{\numberline {A.}Herd Initialization}{11}{subsection.3.1}% -\contentsline {paragraph}{Introduction}{11}{subsection.3.1}% -\contentsline {paragraph}{Methodology}{14}{table.3}% -\contentsline {subsection}{\numberline {B.}Pens and Animal Grouping}{15}{subsection.3.2}% -\contentsline {paragraph}{Introduction}{15}{subsection.3.2}% -\contentsline {paragraph}{Methodology}{17}{table.5}% -\contentsline {paragraph}{Remove\_animals\_by\_ids}{17}{table.caption.2}% -\contentsline {paragraph}{\_add\_new\_animals}{18}{table.caption.2}% -\contentsline {paragraph}{Set\_animal\_nutritional\_requirements}{18}{table.caption.2}% -\contentsline {subsection}{\numberline {C.}Ration Formulation}{18}{subsection.3.3}% -\contentsline {subsubsection}{\numberline {a.}Energy and Nutrition Requirements}{18}{subsubsection.3.3.1}% -\contentsline {paragraph}{NRC: Calculating Nutrient Requirements of Dairy Cattle}{18}{subsubsection.3.3.1}% -\contentsline {subsubsection}{\numberline {b.}Nutrient Requirements of Dairy Cattle (NRC)}{19}{subsubsection.3.3.2}% -\contentsline {paragraph}{NASEM: Calculating Nutrient Requirements of Dairy Cattle: Eighth Revised Edition}{28}{table.9}% -\contentsline {paragraph}{NASEM: Calculating Amino Acid Requirements}{39}{table.12}% -\contentsline {subsubsection}{\numberline {c.}Energy and Nutrition Supply }{43}{subsubsection.3.3.3}% -\contentsline {paragraph}{Nutrient Supply}{43}{subsubsection.3.3.3}% -\contentsline {paragraph}{Energy Supply - NRC 2001}{43}{subsubsection.3.3.3}% -\contentsline {paragraph}{Energy Supply - NASEM 2021}{45}{table.15}% -\contentsline {paragraph}{AA Nutrient Supply}{50}{table.18}% -\contentsline {subsubsection}{\numberline {d.}Automated Ration Formulation}{53}{subsubsection.3.3.4}% -\contentsline {paragraph}{Introduction}{53}{subsubsection.3.3.4}% -\contentsline {paragraph}{Methodology}{55}{table.20}% -\contentsline {subsubsection}{\numberline {e.}User-defined ration formulation}{56}{subsubsection.3.3.5}% -\contentsline {paragraph}{Introduction}{56}{subsubsection.3.3.5}% -\contentsline {paragraph}{Methodology}{56}{table.22}% -\contentsline {subsection}{\numberline {D.}Herd Size Management}{57}{subsection.3.4}% -\contentsline {section}{\numberline {IV.}Animal-level Processes and Management}{59}{section.4}% -\contentsline {paragraph}{Flow of information}{59}{section.4}% -\contentsline {subsection}{\numberline {A.}RuFaS Bodyweight and Growth}{60}{subsection.4.1}% -\contentsline {paragraph}{Introduction}{60}{subsection.4.1}% -\contentsline {paragraph}{Methodology}{61}{table.23}% -\contentsline {paragraph}{Parity 1 Animals:}{63}{table.23}% -\contentsline {paragraph}{Parity 2 Animals}{63}{table.23}% -\contentsline {subsection}{\numberline {B.}Animal Reproduction}{65}{subsection.4.2}% -\contentsline {paragraph}{Introduction}{65}{subsection.4.2}% -\contentsline {paragraph}{Methodology}{69}{table.caption.6}% -\contentsline {subsection}{\numberline {C.}Milk Production}{76}{subsection.4.3}% -\contentsline {paragraph}{Introduction}{76}{subsection.4.3}% -\contentsline {paragraph}{Methodology}{80}{table.30}% -\contentsline {subsection}{\numberline {D.}Lactation Curve: Parameters and Definitions}{84}{subsection.4.4}% -\contentsline {paragraph}{Introduction}{84}{subsection.4.4}% -\contentsline {paragraph}{Methodology}{88}{table.36}% -\contentsline {subsection}{\numberline {E.}Culling}{90}{subsection.4.5}% -\contentsline {paragraph}{Introduction}{90}{subsection.4.5}% -\contentsline {paragraph}{Methodology}{93}{table.37}% -\contentsline {section}{\numberline {V.}Methane Emission and Manure Excretion}{98}{section.5}% -\contentsline {subsection}{\numberline {A.}Manure Excretion}{98}{subsection.5.1}% -\contentsline {paragraph}{Introduction}{98}{subsection.5.1}% -\contentsline {paragraph}{Methodology}{101}{table.42}% -\contentsline {paragraph}{Manure excretions}{101}{table.42}% -\contentsline {paragraph}{Manure nutrient composition}{102}{table.42}% -\contentsline {paragraph}{Manure excretions}{103}{table.42}% -\contentsline {paragraph}{Manure nutrient composition}{104}{table.42}% -\contentsline {paragraph}{Manure excretions}{105}{table.42}% -\contentsline {paragraph}{Manure nutrient composition}{106}{table.42}% -\contentsline {paragraph}{Manure excretions}{107}{table.42}% -\contentsline {subsection}{\numberline {B.}Enteric Methane Emission}{110}{subsection.5.2}% -\contentsline {paragraph}{Introduction}{110}{subsection.5.2}% -\contentsline {paragraph}{Methodology}{111}{table.46}% -\contentsline {paragraph}{Mutian Model}{112}{table.46}% -\contentsline {paragraph}{Mills Model}{112}{table.46}% -\contentsline {paragraph}{IPCC Model}{113}{table.46}% -\contentsline {paragraph}{Mills Model}{113}{table.46}% -\contentsline {paragraph}{IPCC Model}{113}{table.46}% -\contentsline {subsection}{\numberline {C.}Enteric Methane Mitigation}{113}{subsection.5.3}% -\contentsline {paragraph}{Introduction}{113}{subsection.5.3}% -\contentsline {paragraph}{Methodology}{114}{table.50}% -\contentsline {section}{\numberline {VI.}Abbreviations}{116}{section.6}% -\contentsline {section}{\numberline {VII.}References}{118}{section.7}% \@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{} +\etoc@setlocaltop \Etoc@part@@ \babel@toc {english}{}\relax -\contentsline {section}{\numberline {VIII.}Preface: A Day in the Life on a RuFaS Farm}{6}{section.8}% -\contentsline {paragraph}{Feeding the Animals}{6}{section.8}% -\contentsline {paragraph}{Taking Care of the Animals}{6}{section.8}% -\contentsline {paragraph}{Dealing with the Manure}{7}{section.8}% -\contentsline {paragraph}{Managing the Fields}{7}{section.8}% -\contentsline {paragraph}{Storing the Feeds}{7}{section.8}% -\contentsline {section}{\numberline {IX.}Module Introduction}{7}{section.9}% -\contentsline {subsection}{\numberline {A.}Structural setup of the Manure Module}{8}{subsection.9.1}% -\contentsline {subsection}{\numberline {B.}Overview of Required Inputs}{9}{subsection.9.2}% -\contentsline {subsection}{\numberline {C.}General Assumptions of the Manure Module}{10}{subsection.9.3}% -\contentsline {section}{\numberline {X.}Animal and Manure Module Connection}{11}{section.10}% -\contentsline {subsection}{\numberline {A.}Introduction}{11}{subsection.10.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{14}{subsection.10.2}% -\contentsline {section}{\numberline {XI.}Manure Handler}{19}{section.11}% -\contentsline {subsection}{\numberline {A.}Introduction}{19}{subsection.11.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{22}{subsection.11.2}% -\contentsline {subsection}{\numberline {C.}Manure composition update}{28}{subsection.11.3}% -\contentsline {section}{\numberline {XII.}Solid Liquid Separators}{28}{section.12}% -\contentsline {subsection}{\numberline {A.}Introduction}{28}{subsection.12.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{31}{subsection.12.2}% -\contentsline {subsection}{\numberline {C.}Manure composition update}{33}{subsection.12.3}% -\contentsline {section}{\numberline {XIII.}Anaerobic Digestion}{35}{section.13}% -\contentsline {subsection}{\numberline {A.}Introduction}{35}{subsection.13.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{37}{subsection.13.2}% -\contentsline {subsection}{\numberline {C.}Manure composition update}{41}{subsection.13.3}% -\contentsline {section}{\numberline {XIV.}Slurry Storage}{43}{section.14}% -\contentsline {subsection}{\numberline {A.}Introduction}{43}{subsection.14.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{45}{subsection.14.2}% -\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{51}{subsection.14.3}% -\contentsline {subsection}{\numberline {D.}Manure composition updates}{52}{subsection.14.4}% -\contentsline {section}{\numberline {XV.}Anaerobic Lagoon}{53}{section.15}% -\contentsline {subsection}{\numberline {A.}Introduction}{53}{subsection.15.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{55}{subsection.15.2}% -\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{62}{subsection.15.3}% -\contentsline {subsection}{\numberline {D.}Manure composition updates}{62}{subsection.15.4}% -\contentsline {section}{\numberline {XVI.}Bedded Pack}{64}{section.16}% -\contentsline {subsection}{\numberline {A.}Introduction}{64}{subsection.16.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{66}{subsection.16.2}% -\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{71}{subsection.16.3}% -\contentsline {subsection}{\numberline {D.}Manure composition updates}{72}{subsection.16.4}% -\contentsline {section}{\numberline {XVII.}Open Lot}{74}{section.17}% -\contentsline {subsection}{\numberline {A.}Introduction}{74}{subsection.17.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{76}{subsection.17.2}% -\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{81}{subsection.17.3}% -\contentsline {subsection}{\numberline {D.}Manure composition updates}{82}{subsection.17.4}% -\contentsline {section}{\numberline {XVIII.}Composting}{84}{section.18}% -\contentsline {subsection}{\numberline {A.}Introduction}{84}{subsection.18.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{86}{subsection.18.2}% -\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{91}{subsection.18.3}% -\contentsline {subsection}{\numberline {D.}Manure composition updates}{92}{subsection.18.4}% -\contentsline {section}{\numberline {XIX.}Daily spread}{93}{section.19}% -\contentsline {subsection}{\numberline {A.}Introduction}{93}{subsection.19.1}% -\contentsline {section}{\numberline {XX.}Manure to Soil and Crop Module Connection}{95}{section.20}% -\contentsline {subsection}{\numberline {A.}Introduction}{95}{subsection.20.1}% -\contentsline {subsection}{\numberline {B.}Implementation in RuFaS}{95}{subsection.20.2}% -\contentsline {subsection}{\numberline {C.}Methodology}{96}{subsection.20.3}% -\contentsline {section}{\numberline {XXI.}Key Constants}{98}{section.21}% -\contentsline {section}{\numberline {XXII.}Abbreviations}{100}{section.22}% -\contentsline {section}{\numberline {XXIII.}References}{102}{section.23}% -\contentsline {section}{\numberline {XXIV.}Preface: A Day in the Life on a RuFaS Farm}{6}{section.24}% -\contentsline {paragraph}{Feeding the Animals}{6}{section.24}% -\contentsline {paragraph}{Taking Care of the Animals}{6}{section.24}% -\contentsline {paragraph}{Dealing with the Manure}{7}{section.24}% -\contentsline {paragraph}{Managing the Fields}{7}{section.24}% -\contentsline {paragraph}{Storing the Feeds}{7}{section.24}% -\contentsline {section}{\numberline {XXV.}Module Introduction}{8}{section.25}% -\contentsline {section}{\numberline {XXVI.}Field Management}{8}{section.26}% -\contentsline {subsection}{\numberline {A.}Introduction}{8}{subsection.26.1}% -\contentsline {paragraph}{Setting up Field Management}{8}{subsection.26.1}% -\contentsline {paragraph}{Field Management Initialization}{8}{subsection.26.1}% -\contentsline {paragraph}{Field Setup and Initialization}{9}{figure.caption.46}% -\contentsline {paragraph}{Required Inputs}{10}{figure.caption.46}% -\contentsline {subsection}{\numberline {B.}Methodology}{16}{subsection.26.2}% -\contentsline {paragraph}{Daily Field Management}{17}{subsection.26.2}% -\contentsline {paragraph}{Fertilizer Application}{17}{subsection.26.2}% -\contentsline {paragraph}{Where:}{18}{subsection.26.2}% -\contentsline {paragraph}{Where:}{18}{subsection.26.2}% -\contentsline {paragraph}{Where:}{19}{subsection.26.2}% -\contentsline {paragraph}{Where:}{19}{subsection.26.2}% -\contentsline {paragraph}{Manure Application}{20}{subsection.26.2}% -\contentsline {paragraph}{Where:}{20}{subsection.26.2}% -\contentsline {paragraph}{Surface Manure Application}{20}{subsection.26.2}% -\contentsline {paragraph}{Where:}{21}{subsection.26.2}% -\contentsline {paragraph}{Surface Phosphorus Application}{21}{subsection.26.2}% -\contentsline {paragraph}{Where:}{22}{subsection.26.2}% -\contentsline {paragraph}{Surface Nitrogen Application}{22}{subsection.26.2}% -\contentsline {paragraph}{Where:}{22}{subsection.26.2}% -\contentsline {paragraph}{Subsurface Manure Application}{23}{subsection.26.2}% -\contentsline {paragraph}{Tillage Application}{23}{subsection.26.2}% -\contentsline {paragraph}{Initiate Daily Biophysical Processes}{24}{subsection.26.2}% -\contentsline {paragraph}{Crop Management}{24}{subsection.26.2}% -\contentsline {section}{\numberline {XXVII.}Soil Management}{24}{section.27}% -\contentsline {subsection}{\numberline {A.}Introduction}{24}{subsection.27.1}% -\contentsline {paragraph}{Soil Initialization}{24}{subsection.27.1}% -\contentsline {paragraph}{Required Inputs}{25}{subsection.27.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{28}{subsection.27.2}% -\contentsline {paragraph}{Soil Temperature}{28}{subsection.27.2}% -\contentsline {paragraph}{Infiltration (implemented in infiltration.py)}{30}{subsection.27.2}% -\contentsline {paragraph}{Evapotranspiration}{32}{subsection.27.2}% -\contentsline {paragraph}{Potential Evapotranspiration (Implemented in field.py)}{33}{subsection.27.2}% -\contentsline {paragraph}{Percolation (implemented in percolation.py)}{35}{subsection.27.2}% -\contentsline {subsection}{\numberline {C.}Soil Erosion (Implemented as soil\_erosion.py)}{36}{subsection.27.3}% -\contentsline {paragraph}{Base Equation, Rainfall Intensity, and Peak Runoff}{36}{subsection.27.3}% -\contentsline {subsection}{\numberline {D.}Soil Nitrogen Cycling}{40}{subsection.27.4}% -\contentsline {paragraph}{Nitrification and Volatilization (Implemented in nitirification\_volatilization.py)}{42}{subsection.27.4}% -\contentsline {paragraph}{N loss in leaching and runoff (Implemented in leaching\_runoff\_erosion.py)}{44}{subsection.27.4}% -\contentsline {paragraph}{N erosion (Implemented in leaching\_runoff\_erosion.py)}{45}{subsection.27.4}% -\contentsline {paragraph}{Denitrification (Implemented in denitrification.py)}{46}{subsection.27.4}% -\contentsline {subsection}{\numberline {E.}Soil Phosphorus Cycling}{50}{subsection.27.5}% -\contentsline {paragraph}{Phosphorus Initialization (Implemented in layer\_data.py)}{50}{subsection.27.5}% -\contentsline {paragraph}{Soluble Phosphorus (Implemented in soluble\_phosphorus.py)}{51}{subsection.27.5}% -\contentsline {paragraph}{Soluble Phosphorus Runoff}{51}{subsection.27.5}% -\contentsline {paragraph}{Soluble Phosphorus Leaching}{52}{subsection.27.5}% -\contentsline {paragraph}{Fertilizer Leaching and Runoff (Implemented in fertilizer.py)}{53}{subsection.27.5}% -\contentsline {paragraph}{Available Fertilizer P pool }{53}{subsection.27.5}% -\contentsline {paragraph}{Manure Decomposition (implemented in manure\_pool.py)}{57}{subsection.27.5}% -\contentsline {paragraph}{Manure Runoff (implemented in manure\_pool.py)}{60}{subsection.27.5}% -\contentsline {subsection}{\numberline {F.}Soil Carbon Cycling}{63}{subsection.27.6}% -\contentsline {paragraph}{Soil Carbon Partitioning (implemented in carbon\_cycle.py)}{63}{subsection.27.6}% -\contentsline {paragraph}{Decomposition (implemented in decomposition.py)}{64}{subsection.27.6}% -\contentsline {paragraph}{Residue Partitioning (implemented in residue\_partitioning.py)}{67}{subsection.27.6}% -\contentsline {paragraph}{Above Ground: Lignin, Metabolic C, Structural C}{67}{subsection.27.6}% -\contentsline {paragraph}{Pool and Gas Partitioning (implemented in pool\_gas\_partition.py)}{72}{subsection.27.6}% -\contentsline {section}{\numberline {XXVIII.}Crop Management}{76}{section.28}% -\contentsline {subsection}{\numberline {A.}Introduction}{76}{subsection.28.1}% -\contentsline {paragraph}{Planting and Initialization}{76}{subsection.28.1}% -\contentsline {paragraph}{Daily Biophysical Processes}{76}{subsection.28.1}% -\contentsline {paragraph}{Harvest}{76}{subsection.28.1}% -\contentsline {subsection}{\numberline {B.}Methodology}{76}{subsection.28.2}% -\contentsline {paragraph}{Crop Water Cycle Daily Updates}{76}{subsection.28.2}% -\contentsline {paragraph}{Crop Evaporation}{76}{subsection.28.2}% -\contentsline {paragraph}{Crop Canopy Water}{77}{subsection.28.2}% -\contentsline {paragraph}{Crop Potential Transpiration}{77}{subsection.28.2}% -\contentsline {paragraph}{Potential Water Uptake}{78}{subsection.28.2}% -\contentsline {paragraph}{Actual water uptake}{79}{subsection.28.2}% -\contentsline {paragraph}{Maturity}{80}{subsection.28.2}% -\contentsline {paragraph}{Dormancy}{80}{subsection.28.2}% -\contentsline {paragraph}{Accumulation of Heat Units}{81}{subsection.28.2}% -\contentsline {paragraph}{Root Development}{82}{Item.55}% -\contentsline {paragraph}{Potential Nitrogen Uptake}{83}{Item.55}% -\contentsline {paragraph}{Actual Nitrogen Uptake}{84}{Item.55}% -\contentsline {paragraph}{Nitrogen Fixation}{86}{Item.55}% -\contentsline {paragraph}{Store Nitrogen in Plant}{87}{Item.55}% -\contentsline {paragraph}{Water stress}{88}{Item.55}% -\contentsline {paragraph}{Temperature stress}{88}{Item.55}% -\contentsline {paragraph}{Nitrogen and Phosphorus Stress}{89}{Item.55}% -\contentsline {section}{\numberline {XXIX.}Abbreviations}{96}{section.29}% -\contentsline {section}{\numberline {XXX.}Preface: A Day in the Life on a RuFaS Farm}{6}{section.30}% -\contentsline {paragraph}{Feeding the Animals}{6}{section.30}% -\contentsline {paragraph}{Taking Care of the Animals}{6}{section.30}% -\contentsline {paragraph}{Dealing with the Manure}{7}{section.30}% -\contentsline {paragraph}{Managing the Fields}{7}{section.30}% -\contentsline {paragraph}{Storing the Feeds}{7}{section.30}% -\contentsline {section}{\numberline {XXXI.}Module Introduction}{8}{section.31}% -\contentsline {subsection}{\numberline {A.}Feed Quality Assessment}{8}{subsection.31.1}% -\contentsline {section}{\numberline {XXXII.}Feed Storage Inputs}{9}{section.32}% -\contentsline {section}{\numberline {XXXIII.}Storage Classifications}{9}{section.33}% -\contentsline {subsection}{\numberline {A.}Grain}{9}{subsection.33.1}% -\contentsline {subsection}{\numberline {B.}Hay}{10}{subsection.33.2}% -\contentsline {subsection}{\numberline {C.}Silage}{12}{subsection.33.3}% -\contentsline {subsection}{\numberline {D.}Baleage}{15}{subsection.33.4}% -\contentsline {subsection}{\numberline {E.}Nutrient Composition}{15}{subsection.33.5}% -\contentsline {section}{\numberline {XXXIV.}Abbreviations}{16}{section.34}% -\contentsline {section}{\numberline {XXXV.}References}{18}{section.35}% +\contentsline {part}{I\hspace {1em}Preface: A Day in the Life on a RuFaS Farm}{4}{part.1}% +\contentsline {paragraph}{Feeding the Animals}{4}{part.1}% +\contentsline {paragraph}{Taking Care of the Animals}{4}{part.1}% +\contentsline {paragraph}{Dealing with the Manure}{5}{part.1}% +\contentsline {paragraph}{Managing the Fields}{5}{part.1}% +\contentsline {paragraph}{Storing the Feeds}{5}{part.1}% +\contentsline {part}{II\hspace {1em}Animal Module}{6}{part.2}% +\etoc@startlocaltoc {2} +\etoc@startlocaltoc {3} +\etoc@startlocaltoc {4} +\contentsline {section}{\numberline {1}Module Introduction}{10}{section.1}% +\contentsline {subsection}{\numberline {1.a}Animal Life Cycle}{10}{subsection.1.1}% +\contentsline {section}{\numberline {2}Herd-level Processes and Management}{11}{section.2}% +\contentsline {subsection}{\numberline {2.a}Herd Initialization}{11}{subsection.2.1}% +\contentsline {paragraph}{Introduction}{11}{subsection.2.1}% +\contentsline {table}{\numberline {1}{\ignorespaces Overview of the distinct phases by which animals are created and introduced to the herd.}}{12}{table.1}% +\contentsline {table}{\numberline {2}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section}}{13}{table.2}% +\contentsline {table}{\numberline {3}{\ignorespaces User inputs in the animal input file that influence the generation of the Animal Population (pre-animal-population). The inputs of this table are found in the Herd Initialization Section.}}{13}{table.3}% +\contentsline {paragraph}{Methodology}{15}{table.3}% +\contentsline {subsection}{\numberline {2.b}Pens and Animal Grouping}{16}{subsection.2.2}% +\contentsline {paragraph}{Introduction}{16}{subsection.2.2}% +\contentsline {table}{\numberline {4}{\ignorespaces The user must define at least 3 pens and for each pen, key inputs are:}}{17}{table.4}% +\contentsline {paragraph}{Methodology}{18}{table.5}% +\contentsline {table}{\numberline {6}{\ignorespaces A summary of animal types}}{18}{table.caption.2}% +\contentsline {paragraph}{Remove\_animals\_by\_ids}{18}{table.caption.2}% +\contentsline {paragraph}{\_add\_new\_animals}{19}{table.caption.2}% +\contentsline {paragraph}{Set\_animal\_nutritional\_requirements}{19}{table.caption.2}% +\contentsline {subsection}{\numberline {2.c}Ration Formulation}{19}{subsection.2.3}% +\contentsline {subsubsection}{\numberline {2.c.i}Energy and Nutrition Requirements}{19}{subsubsection.2.3.1}% +\contentsline {paragraph}{NRC: Calculating Nutrient Requirements of Dairy Cattle}{19}{subsubsection.2.3.1}% +\contentsline {subsubsection}{\numberline {2.c.ii}Nutrient Requirements of Dairy Cattle (NRC)}{20}{subsubsection.2.3.2}% +\contentsline {table}{\numberline {7}{\ignorespaces Key variables used in protein requirement calculations.}}{25}{table.7}% +\contentsline {table}{\numberline {8}{\ignorespaces Key variables used in mineral requirement calculations.}}{28}{table.8}% +\contentsline {table}{\numberline {9}{\ignorespaces Key variables used in DMI requirement calculations.}}{29}{table.9}% +\contentsline {paragraph}{NASEM: Calculating Nutrient Requirements of Dairy Cattle: Eighth Revised Edition}{29}{table.9}% +\contentsline {table}{\numberline {10}{\ignorespaces Key variables used in protein requirement calculations.}}{35}{table.10}% +\contentsline {table}{\numberline {11}{\ignorespaces Key variables used in mineral requirement calculations.}}{38}{table.11}% +\contentsline {table}{\numberline {12}{\ignorespaces Key variables used in DMI estimation calculations.}}{40}{table.12}% +\contentsline {paragraph}{NASEM: Calculating Amino Acid Requirements}{40}{table.12}% +\contentsline {table}{\numberline {13}{\ignorespaces Essential and non-essential amino acids}}{40}{table.13}% +\contentsline {table}{\numberline {14}{\ignorespaces Key variables used in calculation of AA.}}{42}{table.14}% +\contentsline {subsubsection}{\numberline {2.c.iii}Energy and Nutrition Supply }{44}{subsubsection.2.3.3}% +\contentsline {paragraph}{Nutrient Supply}{44}{subsubsection.2.3.3}% +\contentsline {paragraph}{Energy Supply - NRC 2001}{44}{subsubsection.2.3.3}% +\contentsline {table}{\numberline {15}{\ignorespaces Key variables used in calculation of net energy in NRC 2001.}}{46}{table.15}% +\contentsline {paragraph}{Energy Supply - NASEM 2021}{46}{table.15}% +\contentsline {table}{\numberline {16}{\ignorespaces Key variables used in calculation of net energy supply from NASEM 2021.}}{48}{table.16}% +\contentsline {table}{\numberline {17}{\ignorespaces Key variables used in calculation of AA.}}{51}{table.17}% +\contentsline {table}{\numberline {18}{\ignorespaces Key variables used in calculation of AA.}}{51}{table.18}% +\contentsline {paragraph}{AA Nutrient Supply}{52}{table.18}% +\contentsline {subsubsection}{\numberline {2.c.iv}Automated Ration Formulation}{54}{subsubsection.2.3.4}% +\contentsline {paragraph}{Introduction}{54}{subsubsection.2.3.4}% +\contentsline {table}{\numberline {19}{\ignorespaces Key inputs found in the animal input file.}}{55}{table.caption.3}% +\contentsline {table}{\numberline {20}{\ignorespaces Key inputs found in the feed input file.}}{56}{table.caption.4}% +\contentsline {paragraph}{Methodology}{57}{table.caption.4}% +\contentsline {table}{\numberline {21}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages}}{58}{table.21}% +\contentsline {subsubsection}{\numberline {2.c.v}User-defined ration formulation}{58}{subsubsection.2.3.5}% +\contentsline {paragraph}{Introduction}{58}{subsubsection.2.3.5}% +\contentsline {table}{\numberline {22}{\ignorespaces Key inputs found in the feed input file specific to user defined ration methodology. All are found in the section user\_defined\_ration\_percentages.}}{59}{table.caption.5}% +\contentsline {paragraph}{Methodology}{60}{table.caption.5}% +\contentsline {subsection}{\numberline {2.d}Herd Size Management}{60}{subsection.2.4}% +\contentsline {section}{\numberline {3}Animal-level Processes and Management}{62}{section.3}% +\contentsline {paragraph}{Flow of information}{62}{section.3}% +\contentsline {figure}{\numberline {1}{\ignorespaces There are 5 life stages from calf to cow and a cull stage as outlined in this figure.}}{63}{figure.caption.6}% +\contentsline {subsection}{\numberline {3.a}RuFaS Bodyweight and Growth}{63}{subsection.3.1}% +\contentsline {paragraph}{Introduction}{63}{subsection.3.1}% +\contentsline {table}{\numberline {23}{\ignorespaces Below is a summary of the user inputs that are available and their definitions.}}{64}{table.23}% +\contentsline {paragraph}{Methodology}{64}{table.23}% +\contentsline {paragraph}{Parity 1 Animals:}{66}{table.23}% +\contentsline {paragraph}{Parity 2 Animals}{66}{table.23}% +\contentsline {subsection}{\numberline {3.b}Animal Reproduction}{68}{subsection.3.2}% +\contentsline {paragraph}{Introduction}{68}{subsection.3.2}% +\contentsline {table}{\numberline {24}{\ignorespaces Below are the key user inputs that determine the \textbf {heifer reproductive breeding program} and impact reproductive efficiency and age at first calving.}}{70}{table.caption.8}% +\contentsline {table}{\numberline {25}{\ignorespaces The following inputs determine reproductive efficiency of cows and influence culling, calving interval, and calf output.}}{71}{table.25}% +\contentsline {table}{\numberline {26}{\ignorespaces The following inputs can be used to determine if there is a \textbf {decrease in the conception rate} with parity and rebreeding attempts.}}{72}{table.caption.9}% +\contentsline {paragraph}{Methodology}{73}{table.caption.9}% +\contentsline {figure}{\numberline {2}{\ignorespaces This is a high level schematic to illustrate the methodology behind the heifer breeding and re-breeding in RuFaS Animal Module.}}{74}{figure.caption.10}% +\contentsline {figure}{\numberline {3}{\ignorespaces This is a high level schematic to illustrate the methodology behind the cow breeding and re-breeding in RuFaS Animal Module.}}{76}{figure.caption.11}% +\contentsline {table}{\numberline {27}{\ignorespaces Important functions for the reproduction section.}}{78}{table.27}% +\contentsline {subsection}{\numberline {3.c}Milk Production}{80}{subsection.3.3}% +\contentsline {paragraph}{Introduction}{80}{subsection.3.3}% +\contentsline {table}{\numberline {28}{\ignorespaces The following user inputs are used to estimate customized herd-level lactation curve parameters. See the Methodology section of this document and the Lactation Curve Scientific Documentation for more detail about how these inputs are used with relation to daily milk production.}}{81}{table.28}% +\contentsline {table}{\numberline {29}{\ignorespaces The following inputs are used to determine the milk fat and milk protein percentages for each lactating cow}}{82}{table.29}% +\contentsline {table}{\numberline {30}{\ignorespaces The following inputs are used to constrain how much an average cow’s daily milk production will be reduced due to an inadequate ration. See the Methodology section of this document and the Ration Formulation scientific documentation for more detail about how these inputs are used with relation to daily milk production.}}{83}{table.30}% +\contentsline {paragraph}{Methodology}{84}{table.30}% +\contentsline {figure}{\numberline {4}{\ignorespaces A schematic illustrating the flow of milk reduction in ration formulation logic.}}{87}{figure.caption.12}% +\contentsline {subsection}{\numberline {3.d}Lactation Curve: Parameters and Definitions}{88}{subsection.3.4}% +\contentsline {paragraph}{Introduction}{88}{subsection.3.4}% +\contentsline {table}{\numberline {31}{\ignorespaces Wood's Lactation Curve Base Parameters – These inputs provide the baseline values and variability for Wood’s lactation curve parameters as derived from \blx@tocontentsinit {1}\textcite {Li2022}.}}{90}{table.31}% +\contentsline {table}{\numberline {33}{\ignorespaces Adjustment Factors – These factors adjust the base parameters based on geographical, temporal, management, and parity considerations.}}{91}{table.33}% +\contentsline {table}{\numberline {35}{\ignorespaces Farm Specific 305-Day Milk Production — These inputs help tailor the lactation curve to the farm’s production targets and herd composition.}}{92}{table.35}% +\contentsline {table}{\numberline {36}{\ignorespaces Summary of important functions for the reproduction section. }}{93}{table.36}% +\contentsline {paragraph}{Methodology}{93}{table.36}% +\contentsline {subsection}{\numberline {3.e}Culling}{95}{subsection.3.5}% +\contentsline {paragraph}{Introduction}{95}{subsection.3.5}% +\contentsline {table}{\numberline {37}{\ignorespaces The following inputs are used to determine the probability and timing of cow death and sales events.}}{97}{table.37}% +\contentsline {paragraph}{Methodology}{98}{table.37}% +\contentsline {table}{\numberline {38}{\ignorespaces Cumulative distribution function (CDF) values associated with the conditional probability that a sold animal is removed due to each group of issues and/or the conditional probability of death over time. Corresponds to the “probability” value for each cull reason in the animal input json file. The 'cull\_day\_count' array defines the segments of the CDF}}{102}{table.caption.13}% +\contentsline {section}{\numberline {4}Methane Emission and Manure Excretion}{103}{section.4}% +\contentsline {subsection}{\numberline {4.a}Manure Excretion}{103}{subsection.4.1}% +\contentsline {paragraph}{Introduction}{103}{subsection.4.1}% +\contentsline {table}{\numberline {39}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{104}{table.39}% +\contentsline {table}{\numberline {40}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{104}{table.40}% +\contentsline {table}{\numberline {41}{\ignorespaces These inputs define phosphorus-related outputs relevant to lactating cows.}}{105}{table.41}% +\contentsline {table}{\numberline {42}{\ignorespaces Expected outputs from this section.}}{105}{table.42}% +\contentsline {paragraph}{Methodology}{106}{table.42}% +\contentsline {paragraph}{Manure excretions}{106}{table.42}% +\contentsline {paragraph}{Manure nutrient composition}{107}{table.42}% +\contentsline {paragraph}{Manure excretions}{108}{table.42}% +\contentsline {paragraph}{Manure nutrient composition}{109}{table.42}% +\contentsline {paragraph}{Manure excretions}{110}{table.42}% +\contentsline {paragraph}{Manure nutrient composition}{111}{table.42}% +\contentsline {paragraph}{Manure excretions}{112}{table.42}% +\contentsline {subsection}{\numberline {4.b}Enteric Methane Emission}{115}{subsection.4.2}% +\contentsline {paragraph}{Introduction}{115}{subsection.4.2}% +\contentsline {table}{\numberline {43}{\ignorespaces These inputs define basic animal and diet properties used to calculate nutrient intake and manure production.}}{115}{table.43}% +\contentsline {table}{\numberline {44}{\ignorespaces These inputs are used when modeling cows and are particularly relevant for lactating animals.}}{115}{table.44}% +\contentsline {table}{\numberline {45}{\ignorespaces Inputs specific to the methane emissions model and selected mitigation strategies.}}{116}{table.45}% +\contentsline {table}{\numberline {46}{\ignorespaces Expected outputs from this section.}}{116}{table.46}% +\contentsline {paragraph}{Methodology}{116}{table.46}% +\contentsline {paragraph}{Mutian Model}{117}{table.46}% +\contentsline {paragraph}{Mills Model}{118}{table.46}% +\contentsline {paragraph}{IPCC Model}{118}{table.46}% +\contentsline {paragraph}{Mills Model}{118}{table.46}% +\contentsline {paragraph}{IPCC Model}{118}{table.46}% +\contentsline {subsection}{\numberline {4.c}Enteric Methane Mitigation}{119}{subsection.4.3}% +\contentsline {paragraph}{Introduction}{119}{subsection.4.3}% +\contentsline {table}{\numberline {47}{\ignorespaces General dietary fiber and fat concentration inputs.}}{119}{table.47}% +\contentsline {table}{\numberline {48}{\ignorespaces Feed-based methane mitigation strategies.}}{119}{table.48}% +\contentsline {table}{\numberline {49}{\ignorespaces Dosage of methane mitigation additives.}}{120}{table.49}% +\contentsline {table}{\numberline {50}{\ignorespaces Expected outputs from this section.}}{120}{table.50}% +\contentsline {paragraph}{Methodology}{120}{table.50}% +\contentsline {section}{\numberline {5}References}{122}{section.5}% +\contentsline {part}{III\hspace {1em}Manure Module}{124}{part.3}% +\etoc@startlocaltoc {5} +\etoc@startlocaltoc {6} +\etoc@startlocaltoc {7} +\contentsline {section}{\numberline {6}Module Introduction}{128}{section.6}% +\contentsline {subsection}{\numberline {6.a}Structural setup of the Manure Module}{128}{subsection.6.1}% +\contentsline {table}{\numberline {51}{\ignorespaces Examples of processor types by class.}}{128}{table.caption.14}% +\contentsline {figure}{\numberline {5}{\ignorespaces A real-world example of a simplistic manure management chain. }}{129}{figure.caption.15}% +\contentsline {figure}{\numberline {6}{\ignorespaces The manure management chain illustrated in the previous figure, with RuFaS-specific information reflected. }}{129}{figure.caption.16}% +\contentsline {subsection}{\numberline {6.b}Overview of Required Inputs}{129}{subsection.6.2}% +\contentsline {subsection}{\numberline {6.c}General Assumptions of the Manure Module}{130}{subsection.6.3}% +\contentsline {section}{\numberline {7}Animal and Manure Module Connection}{131}{section.7}% +\contentsline {subsection}{\numberline {7.a}Introduction}{131}{subsection.7.1}% +\contentsline {table}{\numberline {52}{\ignorespaces List of Python classes for Animal to Manure Module connection.}}{131}{table.caption.17}% +\contentsline {table}{\numberline {53}{\ignorespaces User inputs for Stream Formation and Bedding sections.}}{132}{table.53}% +\contentsline {subsection}{\numberline {7.b}Methodology}{134}{subsection.7.2}% +\contentsline {figure}{\numberline {7}{\ignorespaces If manure from a pen is routed to two different general manure streams, two sets of manure stream inputs must be defined. An example of a single pen’s manure stream inputs is above - in this example, manure from this pen is routed to two locations, one representing an exercise lot, the other representing a bedded pack area.}}{135}{figure.caption.18}% +\contentsline {table}{\numberline {54}{\ignorespaces Recommended minutes\_away\_for\_milking by pen type based on published literature. Remember, this does not necessarily reflect the model defaults. }}{138}{table.caption.19}% +\contentsline {table}{\numberline {55}{\ignorespaces Proportions of differnt streams for different animal classes.}}{139}{table.caption.20}% +\contentsline {table}{\numberline {56}{\ignorespaces Calculated manure and bedding characteristics}}{140}{table.caption.21}% +\contentsline {section}{\numberline {8}Manure Handler}{140}{section.8}% +\contentsline {subsection}{\numberline {8.a}Introduction}{140}{subsection.8.1}% +\contentsline {table}{\numberline {57}{\ignorespaces The classes of handlers that are used in this module.}}{142}{table.caption.22}% +\contentsline {table}{\numberline {58}{\ignorespaces Required inputs for the Manure Handler (refreshed\_manure\_management.json)}}{142}{table.caption.23}% +\contentsline {subsection}{\numberline {8.b}Methodology}{144}{subsection.8.2}% +\contentsline {table}{\numberline {59}{\ignorespaces The surface area per stall that is covered with manure is a function of the pen type and type of animal housed.}}{146}{table.caption.24}% +\contentsline {subsection}{\numberline {8.c}Manure composition update}{149}{subsection.8.3}% +\contentsline {table}{\numberline {60}{\ignorespaces Calculated manure storage variables and their units}}{149}{table.caption.25}% +\contentsline {section}{\numberline {9}Solid Liquid Separators}{149}{section.9}% +\contentsline {subsection}{\numberline {9.a}Introduction}{149}{subsection.9.1}% +\contentsline {table}{\numberline {61}{\ignorespaces List of Python classes for solid liquid separators.}}{150}{table.caption.26}% +\contentsline {table}{\numberline {62}{\ignorespaces The required inputs of this section.}}{151}{table.62}% +\contentsline {subsection}{\numberline {9.b}Methodology}{152}{subsection.9.2}% +\contentsline {table}{\numberline {63}{\ignorespaces The default, minimums, and maximums for various separation efficiencies.}}{153}{table.caption.27}% +\contentsline {subsection}{\numberline {9.c}Manure composition update}{154}{subsection.9.3}% +\contentsline {table}{\numberline {64}{\ignorespaces Solids and liquid fraction calculations for separated manure components}}{154}{table.64}% +\contentsline {section}{\numberline {10}Anaerobic Digestion}{156}{section.10}% +\contentsline {subsection}{\numberline {10.a}Introduction}{156}{subsection.10.1}% +\contentsline {table}{\numberline {65}{\ignorespaces List of Python classes for anaerobic digestors.}}{157}{table.caption.28}% +\contentsline {table}{\numberline {66}{\ignorespaces Required inputs for this section.}}{157}{table.caption.29}% +\contentsline {subsection}{\numberline {10.b}Methodology}{158}{subsection.10.2}% +\contentsline {subsection}{\numberline {10.c}Manure composition update}{162}{subsection.10.3}% +\contentsline {table}{\numberline {67}{\ignorespaces Calculated anaerobic digestion outputs.}}{163}{table.67}% +\contentsline {section}{\numberline {11}Slurry Storage}{164}{section.11}% +\contentsline {subsection}{\numberline {11.a}Introduction}{164}{subsection.11.1}% +\contentsline {table}{\numberline {68}{\ignorespaces Key differences for two options of slurry storage.}}{164}{table.caption.30}% +\contentsline {table}{\numberline {69}{\ignorespaces Required inputs for the slurry storage section.}}{165}{table.caption.32}% +\contentsline {subsection}{\numberline {11.b}Methodology}{166}{subsection.11.2}% +\contentsline {subsection}{\numberline {11.c}Received, stored, and emptied outputs}{172}{subsection.11.3}% +\contentsline {subsection}{\numberline {11.d}Manure composition updates}{173}{subsection.11.4}% +\contentsline {table}{\numberline {70}{\ignorespaces Manure storage variable calculations}}{173}{table.70}% +\contentsline {section}{\numberline {12}Anaerobic Lagoon}{174}{section.12}% +\contentsline {subsection}{\numberline {12.a}Introduction}{174}{subsection.12.1}% +\contentsline {table}{\numberline {71}{\ignorespaces List of Python classes for anaerobic lagoon.}}{175}{table.caption.33}% +\contentsline {table}{\numberline {72}{\ignorespaces Required inputs for the anaerobic lagoon section (refreshed\_manure\_management.json)}}{175}{table.caption.34}% +\contentsline {subsection}{\numberline {12.b}Methodology}{176}{subsection.12.2}% +\contentsline {subsection}{\numberline {12.c}Received, stored, and emptied outputs}{183}{subsection.12.3}% +\contentsline {subsection}{\numberline {12.d}Manure composition updates}{183}{subsection.12.4}% +\contentsline {table}{\numberline {73}{\ignorespaces Manure storage variable calculations}}{184}{table.73}% +\contentsline {section}{\numberline {13}Bedded Pack}{185}{section.13}% +\contentsline {subsection}{\numberline {13.a}Introduction}{185}{subsection.13.1}% +\contentsline {table}{\numberline {74}{\ignorespaces List of classes for bedded pack.}}{186}{table.caption.35}% +\contentsline {table}{\numberline {75}{\ignorespaces Required inputs for the bedded pack section (refreshed\_manure\_management.json)}}{186}{table.caption.36}% +\contentsline {subsection}{\numberline {13.b}Methodology}{187}{subsection.13.2}% +\contentsline {table}{\numberline {76}{\ignorespaces Methane conversion factor values for bedded pack pens, based on presence or absence of mixing and average annual air temperature.}}{187}{table.caption.37}% +\contentsline {subsection}{\numberline {13.c}Received, stored, and emptied outputs}{192}{subsection.13.3}% +\contentsline {subsection}{\numberline {13.d}Manure composition updates}{193}{subsection.13.4}% +\contentsline {table}{\numberline {77}{\ignorespaces Calculated manure storage variables and their units}}{194}{table.77}% +\contentsline {section}{\numberline {14}Open Lot}{195}{section.14}% +\contentsline {subsection}{\numberline {14.a}Introduction}{195}{subsection.14.1}% +\contentsline {table}{\numberline {78}{\ignorespaces Classes available in open lots.}}{196}{table.caption.38}% +\contentsline {table}{\numberline {79}{\ignorespaces Required inputs for the open lots section}}{196}{table.caption.39}% +\contentsline {subsection}{\numberline {14.b}Methodology}{197}{subsection.14.2}% +\contentsline {subsection}{\numberline {14.c}Received, stored, and emptied outputs}{202}{subsection.14.3}% +\contentsline {subsection}{\numberline {14.d}Manure composition updates}{203}{subsection.14.4}% +\contentsline {table}{\numberline {80}{\ignorespaces Calculated manure storage variables and their units}}{203}{table.80}% +\contentsline {section}{\numberline {15}Composting}{205}{section.15}% +\contentsline {subsection}{\numberline {15.a}Introduction}{205}{subsection.15.1}% +\contentsline {table}{\numberline {81}{\ignorespaces Classes available in composting.}}{205}{table.caption.40}% +\contentsline {table}{\numberline {82}{\ignorespaces Required inputs for the composting section (refreshed\_manure\_management.json)}}{206}{table.caption.41}% +\contentsline {subsection}{\numberline {15.b}Methodology}{207}{subsection.15.2}% +\contentsline {table}{\numberline {83}{\ignorespaces Methane conversion factor values for compost pens, based on composting method and average annual air temperature.}}{207}{table.caption.42}% +\contentsline {table}{\numberline {84}{\ignorespaces NH\textsubscript {3}-N emission factors for compost by composting method.}}{211}{table.caption.43}% +\contentsline {table}{\numberline {85}{\ignorespaces N\textsubscript {2}O-N emission factors for compost by composting method.}}{212}{table.caption.45}% +\contentsline {subsection}{\numberline {15.c}Received, stored, and emptied outputs}{212}{subsection.15.3}% +\contentsline {subsection}{\numberline {15.d}Manure composition updates}{213}{subsection.15.4}% +\contentsline {table}{\numberline {86}{\ignorespaces Manure storage variable calculations}}{213}{table.86}% +\contentsline {section}{\numberline {16}Daily spread}{215}{section.16}% +\contentsline {subsection}{\numberline {16.a}Introduction}{215}{subsection.16.1}% +\contentsline {table}{\numberline {87}{\ignorespaces List of classes for daily spread.}}{215}{table.caption.46}% +\contentsline {table}{\numberline {88}{\ignorespaces Required inputs for the daily spread section (refreshed\_manure\_management.json)}}{215}{table.caption.47}% +\contentsline {section}{\numberline {17}Manure to Soil and Crop Module Connection}{217}{section.17}% +\contentsline {subsection}{\numberline {17.a}Introduction}{217}{subsection.17.1}% +\contentsline {subsection}{\numberline {17.b}Implementation in RuFaS}{217}{subsection.17.2}% +\contentsline {figure}{\numberline {8}{\ignorespaces \relax }}{218}{figure.caption.48}% +\contentsline {subsection}{\numberline {17.c}Methodology}{218}{subsection.17.3}% +\contentsline {section}{\numberline {18}Key Constants}{221}{section.18}% +\contentsline {table}{\numberline {89}{\ignorespaces The key constants for all equations in the Manure Module}}{221}{table.89}% +\contentsline {section}{\numberline {19}References}{224}{section.19}% +\contentsline {part}{IV\hspace {1em}Soil and Crop Module}{226}{part.4}% +\etoc@startlocaltoc {8} +\etoc@startlocaltoc {9} +\etoc@startlocaltoc {10} +\contentsline {section}{\numberline {20}Module Introduction}{229}{section.20}% +\contentsline {section}{\numberline {21}Field Management}{229}{section.21}% +\contentsline {subsection}{\numberline {21.a}Introduction}{229}{subsection.21.1}% +\contentsline {paragraph}{Setting up Field Management}{229}{subsection.21.1}% +\contentsline {paragraph}{Field Management Initialization}{229}{subsection.21.1}% +\contentsline {figure}{\numberline {9}{\ignorespaces Example of the metadata input file.}}{230}{figure.caption.49}% +\contentsline {paragraph}{Field Setup and Initialization}{230}{figure.caption.49}% +\contentsline {paragraph}{Required Inputs}{231}{figure.caption.49}% +\contentsline {table}{\numberline {90}{\ignorespaces Required user inputs for the FieldManager section.}}{231}{table.90}% +\contentsline {subsection}{\numberline {21.b}Methodology}{237}{subsection.21.2}% +\contentsline {paragraph}{Daily Field Management}{238}{subsection.21.2}% +\contentsline {paragraph}{Fertilizer Application}{239}{subsection.21.2}% +\contentsline {paragraph}{Where:}{239}{subsection.21.2}% +\contentsline {paragraph}{Where:}{239}{subsection.21.2}% +\contentsline {paragraph}{Where:}{240}{subsection.21.2}% +\contentsline {paragraph}{Where:}{241}{subsection.21.2}% +\contentsline {paragraph}{Manure Application}{241}{subsection.21.2}% +\contentsline {paragraph}{Where:}{242}{subsection.21.2}% +\contentsline {paragraph}{Surface Manure Application}{242}{subsection.21.2}% +\contentsline {paragraph}{Where:}{242}{subsection.21.2}% +\contentsline {paragraph}{Surface Phosphorus Application}{242}{subsection.21.2}% +\contentsline {paragraph}{Where:}{243}{subsection.21.2}% +\contentsline {paragraph}{Surface Nitrogen Application}{243}{subsection.21.2}% +\contentsline {paragraph}{Where:}{244}{subsection.21.2}% +\contentsline {paragraph}{Subsurface Manure Application}{244}{subsection.21.2}% +\contentsline {paragraph}{Tillage Application}{245}{subsection.21.2}% +\contentsline {paragraph}{Initiate Daily Biophysical Processes}{245}{subsection.21.2}% +\contentsline {paragraph}{Crop Management}{245}{subsection.21.2}% +\contentsline {section}{\numberline {22}Soil Management}{245}{section.22}% +\contentsline {subsection}{\numberline {22.a}Introduction}{245}{subsection.22.1}% +\contentsline {paragraph}{Soil Initialization}{246}{subsection.22.1}% +\contentsline {paragraph}{Required Inputs}{247}{subsection.22.1}% +\contentsline {table}{\numberline {91}{\ignorespaces Required inputs for the Soil section.}}{247}{table.91}% +\contentsline {subsection}{\numberline {22.b}Methodology}{250}{subsection.22.2}% +\contentsline {paragraph}{Soil Temperature}{250}{subsection.22.2}% +\contentsline {paragraph}{Infiltration (implemented in infiltration.py)}{252}{subsection.22.2}% +\contentsline {paragraph}{Evapotranspiration}{254}{subsection.22.2}% +\contentsline {paragraph}{Potential Evapotranspiration (Implemented in field.py)}{255}{subsection.22.2}% +\contentsline {paragraph}{Percolation (implemented in percolation.py)}{257}{subsection.22.2}% +\contentsline {subsection}{\numberline {22.c}Soil Erosion (Implemented as soil\_erosion.py)}{258}{subsection.22.3}% +\contentsline {paragraph}{Base Equation, Rainfall Intensity, and Peak Runoff}{258}{subsection.22.3}% +\contentsline {subsection}{\numberline {22.d}Soil Nitrogen Cycling}{262}{subsection.22.4}% +\contentsline {paragraph}{Nitrification and Volatilization (Implemented in nitirification\_volatilization.py)}{264}{subsection.22.4}% +\contentsline {paragraph}{N loss in leaching and runoff (Implemented in leaching\_runoff\_erosion.py)}{266}{subsection.22.4}% +\contentsline {paragraph}{N erosion (Implemented in leaching\_runoff\_erosion.py)}{267}{subsection.22.4}% +\contentsline {paragraph}{Denitrification (Implemented in denitrification.py)}{268}{subsection.22.4}% +\contentsline {subsection}{\numberline {22.e}Soil Phosphorus Cycling}{272}{subsection.22.5}% +\contentsline {paragraph}{Phosphorus Initialization (Implemented in layer\_data.py)}{272}{subsection.22.5}% +\contentsline {paragraph}{Soluble Phosphorus (Implemented in soluble\_phosphorus.py)}{273}{subsection.22.5}% +\contentsline {paragraph}{Soluble Phosphorus Runoff}{273}{subsection.22.5}% +\contentsline {paragraph}{Soluble Phosphorus Leaching}{274}{subsection.22.5}% +\contentsline {paragraph}{Fertilizer Leaching and Runoff (Implemented in fertilizer.py)}{275}{subsection.22.5}% +\contentsline {paragraph}{Available Fertilizer P pool }{275}{subsection.22.5}% +\contentsline {paragraph}{Manure Decomposition (implemented in manure\_pool.py)}{279}{subsection.22.5}% +\contentsline {paragraph}{Manure Runoff (implemented in manure\_pool.py)}{282}{subsection.22.5}% +\contentsline {subsection}{\numberline {22.f}Soil Carbon Cycling}{285}{subsection.22.6}% +\contentsline {paragraph}{Soil Carbon Partitioning (implemented in 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-\author{ } -\setlength{\topskip}{10pt} % Ensures LaTeX reserves room above the first line -%\usepackage{showframe} - -\begin{document} - -% Custom Title Page -\begin{titlepage} - \thispagestyle{empty} - \centering - \vspace*{2cm} - - {\Huge\bfseries Ruminant Farm System Model\par} - \vspace{1cm} - - {\Large Manure Module\par} - \vspace{1cm} - - {\large \today\par} - \vspace{1.5cm} % Add space before the image - - \includegraphics[width=0.25\textwidth]{resources/manure.png} % Adjust size and filename - - \vfill - - {\small v.1; Updated 2025\par} - \vspace*{1cm} -\end{titlepage} - -% Continue with front matter (e.g., table of contents) -\thispagestyle{fancy} % Ensure the header/footer appears on the first page - +\part{Manure Module} % Global Table of Contents \thispagestyle{fancy} -\tableofcontents -\newpage -\listoffigures +% Local TOC that includes only what’s inside THIS section +\etocsettocstyle{\subsection*{Contents}}{} % heading for the local toc +\etocsetnexttocdepth{subsection} % or subsubsection +\localtableofcontents \newpage -\listoftables +\section*{List of Figures} +\locallistoffigures \newpage - - -\section{Preface: A Day in the Life on a RuFaS Farm} - -This document provides a high-level overview of the daily operations of a ruminant farm, as modeled by RuFaS. The overview will be through the eyes of Dr. Rue Fas. One day, Dr. Rue woke up and decided the life of a computer scientist wasn’t for her. So she bought a dairy farm, and this is how she operates it every day. - -\paragraph{Feeding the Animals} -Second thing in the morning, after coffee, Dr. Rue checks the calendar to see if it’s time to formulate a new ration for her animals. -\vspace{0.2cm} - -If a new ration needs to be formulated, Dr. Rue heads over to the barn where she keeps all her forages and feed. While there, she checks how well all the forages are holding up. After considering the feeds available, the quality of each one, and how much each one costs, she decides on how productive she wants her animals to be. It is a difficult balancing act, but eventually a ration recipe is found that will keep the animals happy while keeping costs low and sustainability high until the calendar says the ration recipe needs to be reformulated. -\vspace{0.2cm} - -When Dr. Rue doesn’t need to formulate a new ration, she takes the last ration recipe she made and grabs all the feed and forage the animals need for the day out of the feed barn. If there isn’t enough for the animals, then a new ration is formulated using the steps above. - -\paragraph{Taking Care of the Animals} -After making sure all the animals’ feed is taken care of, Dr. Rue moves on to taking care of all the other animal tasks. This includes milking the animals, making sure they’re healthy, getting them pregnant, and numerous other tasks. -\vspace{0.2cm} - -As dawn breaks on the RuFaS farm, the animals awaken after a restful night. Joe, the farm master, prepares a large whiteboard to track HerdReproductionStatistics, ensuring he has all the data he needs for the day’s activities. - -\textit{Daily Routine} - After leaving their pens, each animal lines up in front of the barn. Julie, the diligent farm veterinarian, examines them one by one. This daily check includes updates on the following areas: -\begin{itemize} - \item Nutrients: Each animal begins its day with a quick phosphorus requirement assessment. Julie records these details and updates the animal’s phosphorus-related metrics. - \item Digestive System: With nutrient information in hand, Julie shifts focus to each animal’s digestive system, estimating manure output and enteric methane production for that day. - - \item Milk Production: All milking cows are assessed to gauge daily milk yield and milk component content (fat and protein). Any necessary adjustments are noted. - - \item Animal Growth: Around midday, Julie returns to each animal to evaluate daily weight changes. She updates each animal’s body weight accordingly. - - \item Reproduction: HeiferII and Cow stage animals undergo a reproduction check. Julie closely monitors their reproductive progress and updates the HerdReproductionStatistics details on Joe’s whiteboard. - - \item Life Stage Evaluation: Once the daily routines are complete, Julie determines if any animal is ready to progress to the next life stage. Graduating animals are marked as “graduated” to be moved to their new pens. Animals that must leave the herd—due to health, productivity, or other issues—are labeled as “sold” or “dead” to be removed from the farm population. - - \item Herd Size Maintenance: After every animal has been evaluated, Joe counts the herd to ensure it remains at a healthy size. If it is too large, he arranges the sale of some animals. If the herd is too small, he may opt to purchase additional heiferIIIs to keep numbers at the ideal level. - - \item Herd Structure Management: Joe also manages pen assignments. Newly graduated or newborn animals are guided to suitable pens, while animals marked for removal (sold or deceased) are taken out of the herd and removed from the farm records. -\end{itemize} - - -\textit{Output Reporting} -At day’s end, Joe and Julie review the updated HerdReproductionStatistics on the whiteboard. Joe then compiles a concise report summarizing the day’s herd stats. He forwards this information to the OutputManager before wrapping up another successful day on the RuFaS farm. -\vspace{0.5cm} - -\paragraph{Dealing with the Manure} -Once all the animal chores are finished, Dr. Rue moves on to handling the manure. There are a lot of different ways that manure is collected from the animals: it is flushed out of the milking parlor with water, some of the pens need to have it shoveled out along with the bedding in the pen, and some pens have grates that allow the manure to go straight into a pit beneath the barn. -\vspace{0.2cm} - -There are a lot of different places where manure is processed and stored on the farm. Dr. Rue goes from place to place on the farm, moving the manure from one place to the next. The manure chores are finished after moving all of the manure into her lagoons, compost piles, and other storages. As this final manure chore is completed, she writes down all the information about how much manure is in all these storages, and some information about what that manure is made of. How much water, nitrogen, phosphorus, other solids, etc. are in each storage. - -\paragraph{Managing the Fields} -Now that Dr. Rue is done making sure all the manure has been handled and stored properly, she can take care of all the field tasks. She has a lot of fields on her farm, each with its own unique schedule. Her field management routine starts with checking each field’s schedule to see if any of them are due to have manure applied, and if so, how much they should have applied. After noting all the manure that is supposed to go onto her fields, these amounts are checked against the amounts of manure that are in her manure storage. Dr. Rue then applies manure to each field on the schedule that day, trying to match the amount applied to the amount on the schedule as best she can. -\vspace{0.2cm} - -After making sure every manure item on each farm’s schedule has been taken care of for the day, the schedule for each field is rechecked, one field at a time. In each schedule she checks to see if that field needs to be tilled, if any chemical fertilizer needs to be applied, and if any crops need to be planted or harvested. After all these activities are taken care of, Mother Nature goes to work. The sun shines and rain falls, providing the field with water and energy that grows crops and soaks the soil. After taking care of each field one by one, Dr. Rue drives back to the main farm with all of the crops that she harvested on that day. - -\paragraph{Storing the Feeds} -Now that she is back at the barns, all the crops that were just harvested can be stored. Fortunately she is very organized, so all her harvested crops are separate from one another and each has a label, indicating where it will be stored inside the feed barn. As each feed is stored, it is labeled with the current date. Dr. Rue is exhausted from another long day. She goes back to the farmhouse and rests up, preparing to do the whole thing over again tomorrow. Her daily routine might seem repetitive, but each day is a crucial part of the larger, continuous process that keeps her farm running efficiently and sustainably. - +\section*{List of Tables} +\locallistoftables +\newpage \section{Module Introduction} \begin{refsection} - +\par\noindent\justifying The responsibility of the manure module in RuFaS is to simulate the loss and/or gain of manure mass and nutrients on a daily timestep at each step of the manure management chain on a dairy farm. On the majority of farms, manure represents an important link in the cycling of nutrients through animals, land, crops, and back to animals. Therefore, modeling both greenhouse gas (GHG) emissions as well as non-GHG nutrient and losses is crucial in capturing nutrient flows through the whole-farm system. The manure module accomplishes its responsibilities by tracking a critical, core set of variables called “ManureStream” variables, which include key agronomic nutrients (N, P, K), carbon (e.g. total and volatile solids), water, ash, mass, and volume. The Manure Module receives manure excretion and bedding information from the animal module, then passes manure through the manure management chain, until manure is either applied to fields or exported. The specific steps of the manure management chain are user-defined, and the individual steps/options in manure management chains are referred to as “processors”. The exact chemical, physical, or other processes that occur at each step along the management chain depend on what type of processor the manure is being held in. For example, parlor cleaning processors, which represent removing manure from the milking parlor and holding areas, principally add water to manure but do not estimate GH emissions or other nutrient losses. A slurry storage outdoor processor (a type of manure storage), however, estimates daily methane (CH\textsubscript{4}) and ammonia (NH\textsubscript{3}-N) losses, which are then reflected by reducing the quantity of nutrients remaining in the stored manure at the end of the day. @@ -281,8 +59,7 @@ \subsection{Structural setup of the Manure Module} \centering \includegraphics[width=0.9\textwidth]{resources/manuremanchain.png} % Replace with your image file \caption{A real-world example of a simplistic manure management chain. } - \label{fig:manchain} - \end{figure} + \end{figure} @@ -310,7 +87,7 @@ \subsection{Overview of Required Inputs} \vspace{0.2cm} \begin{tcolorbox}[colback=white, colframe=black, boxrule=0.5pt, arc=3pt, width=\textwidth] -The assignment of manure generated in the Animal Module (which also reflects the quantity of bedding used) to its destination in the Manure Module occurs in the Animal Module. See the \hyperref[AnimalManureConn]{Animal to Manure Connection} section for more information. +The assignment of manure generated in the Animal Module (which also reflects the quantity of bedding used) to its destination in the Manure Module occurs in the Animal Module. See the Animal to Manure Connection section for more information. \end{tcolorbox} \vspace{0.2cm} @@ -337,7 +114,7 @@ \subsection{General Assumptions of the Manure Module} \end {enumerate} -\section{Animal and Manure Module Connection} \label{AnimalManureConn} +\section{Animal and Manure Module Connection} \subsection{Introduction} Though animals are typically fed and managed in groups, referred to as pens in RuFaS, manure from a single group of animals may not always remain in or be transported to the same location on the farm. For example, lactating cows who must travel to a milking parlor deposit some proportion of their manure outside of their pen. Or, in open lot systems, manure deposited in the concrete feed alley apron is often removed and managed separately from manure deposited on the lot surface. Additionally, more than one type of bedding may be used in a pen (e.g., no bedding during summer but straw provided in winter), which also eventually becomes part of manure. Considering this, RuFaS accommodates routing of manure from a single group (pen) of animals to multiple locations, which are then received by the Manure module. This document describes how a pen’s total manure excretion and bedding are allocated to one or more discrete quantities of manure, referred to as manure streams, and passed to the Manure module. How the user configures this manure routing and bedding options and addition of bedding to manure are also described here. @@ -613,14 +390,12 @@ \subsection{Methodology} \vspace{0.1cm} -\begin{table}[h!] +\clearpage +\begin{sidewaystable} + \caption{Recommended minutes\_away\_for\_milking by pen type based on published literature. Remember, this does not necessarily reflect the model defaults. } \centering \renewcommand{\arraystretch}{1.3} -\begin{center} - \caption{Recommended minutes\_away\_for\_milking by pen type based on published literature. Remember, this does not necessarily reflect the model defaults. } -\end{center}\ -\vspace{-1cm} \begin{tabular}{@{} L{2cm} L{4cm} L{1.5cm} L{8cm} @{}} \toprule @@ -644,7 +419,7 @@ \subsection{Methodology} \end{tabular} -\end{table} +\end{sidewaystable} @@ -840,7 +615,7 @@ \subsection{Methodology} -\section{Manure Handler} \label{sec:Manure Handler} +\section{Manure Handler} \subsection{Introduction} \vspace{0.2cm} @@ -1382,7 +1157,7 @@ \subsection{Manure composition update} -\section{Solid Liquid Separators} \label{sec:Solid Liquid Separators} +\section{Solid Liquid Separators} \subsection{Introduction} A solid-liquid separator (SLS) is a specialized piece of equipment or system designed to separate larger, solid particles from the liquid component of manure. This type of system may be implemented for a variety of reasons, such as to improve ease of handling of manure liquid, improve the nutrient concentration in manure liquid, reduce storage volume required for manure lagoons or other storage systems, prevent solid accumulation in a covered manure storage, or reclaim manure solids for use as bedding or compost. The solid fraction of manure slurry is composed of fibers originating primarily from manure, but also from feed, bedding, and other environmental sources. Once mechanically separated, the moisture content of the solid fraction ranges from 70\% to 90\%, depending on the specific separator system used. To further reduce moisture content of the separated solids, an additional dewatering or drying step may be incorporated. Manure solids may be directly used or sold for animal bedding (after stabilization), composted, or land applied. @@ -1732,7 +1507,7 @@ \subsection{Manure composition update} -\section{Anaerobic Digestion} \label{sec:Anaerobic Digestion} +\section{Anaerobic Digestion} \subsection{Introduction} Anaerobic digestion is a process where dairy cow manure is treated in an oxygen-free (anaerobic) environment to produce biogas, containing approximately 60\% CH\textsubscript{4}, 40\% CO\textsubscript{2}, which can be utilized as an on-farm or exported energy source. Additional benefits of anaerobic digestion include reduced manure odor, improved stability and quality of manure for fertilization purposes, and reductions in nutrient losses via undesirable greenhouse gas emissions. @@ -2199,7 +1974,7 @@ \subsection{Manure composition update} \newpage -\section{Slurry Storage} \label{sec:Slurry Storage} +\section{Slurry Storage} \subsection{Introduction} Manure that is stored and managed at ~7 to 12\% dry matter is generally considered to be “slurry” manure. Several common options exist for storing manure at this \%DM range. Slurry may be stored in underfloor pits, where manure is deposited directly into the pit through slatted floors, or is moved to an underfloor storage via scrapers or other manure handling systems. Manure may also be transported to outdoor storage tanks or pits/basins, which may be covered or uncovered. \vspace{0.2cm} @@ -2778,7 +2553,7 @@ \subsection{Manure composition updates} \newpage -\section{Anaerobic Lagoon} \label{sec:Anaerobic Lagoon} +\section{Anaerobic Lagoon} \subsection{Introduction} Manure that is stored and managed at less than \~5\% dry matter is generally considered to be liquid manure. Liquid manure is generated by either dilution of raw or slurry manure, generally through the addition of wash or flush water, or removal of a portion of manure solids through solid liquid separation methods (mechanical separator, settling basin, etc.) or anaerobic digestion. Liquid manure is generally stored in a type of large, outdoor storage structure called an anaerobic lagoon, or simply a lagoon. Anaerobic lagoons are not simply structures in which to store manure. Lagoons facilitate biological breakdown of organic materials, which reduces volatile solids content and odor, though also increases N mineralization and loss as ammonia, particularly if the lagoon is uncovered. Accordingly, anaerobic lagoons have specific design and management requirements to facilitate biological treatment activity \parencite{NRCS2017}. Some characteristics that separate an anaerobic lagoon from slurry or liquid manure storage are: @@ -2985,7 +2760,7 @@ \subsection{Methodology} \item No cover \end{itemize} -Detailed descriptions are outlined in the \hyperref[sec:Slurry Storage]{Slurry Storage} section of this module. Precipitation volume for anaerobic lagoons that are uncovered or have a crust is calculated as follows:\\ +Detailed descriptions are outlined in the Slurry Storage section of this module. Precipitation volume for anaerobic lagoons that are uncovered or have a crust is calculated as follows:\\ \vspace{0.5cm} \begin{center} @@ -5097,8 +4872,11 @@ \subsection{Methodology} The projected manure mass is then calculated as: \begin{equation} \text{projected manure mass} = \min\left( \text{mass\_N\_requested}, \text{mass\_P\_requested} \right) -\label{MN.MSC.1} \end{equation} +\vspace{0.5cm} + + {\raggedleft \textbf{[MN.MSC.1]}\par} + \vspace{0.5cm} where: \begin{itemize} @@ -5118,8 +4896,10 @@ \subsection{Methodology} \frac{\text{mass\_requested\_nutrient}}{\text{manure\_nutrient\_available}}, 1 \right) -\label{MN.MSC.2} \end{equation} +\vspace{0.5cm} + + {\raggedleft \textbf{[MN.MSC.2]}\par} \vspace{0.2cm} \textbf{Step 3: Removal of Nutrients from Individual Storages} @@ -5130,8 +4910,11 @@ \subsection{Methodology} \begin{equation} \text{nutrient\_to\_be\_removed\_from\_storage} = \text{nutrient\_in\_storage} \times \text{nutrient\_proportion\_to\_be\_removed} -\label{MN.MSC.3} \end{equation} +\vspace{0.5cm} + + {\raggedleft \textbf{[MN.MSC.3]}\par} + \vspace{0.5cm} where: \begin{itemize} @@ -5235,103 +5018,6 @@ \section{Key Constants} \end{longtable} \end{landscape} -\newpage -\section{Abbreviations} - -\renewcommand{\arraystretch}{1.3} -\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}} - -\begin{longtable}{@{} L{4cm} L{12cm} @{}} -\caption{Common abbreviations used throughout this document} \\ - -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endfirsthead - -\multicolumn{2}{@{}l}{\textit{Table continued from previous page}} \\ -\toprule -\textbf{Abbreviation} & \textbf{Full Term or Phrase} \\ -\midrule -\endhead - -\midrule -\multicolumn{2}{@{}r@{}}{\textit{Continued on next page}} \\ -\endfoot - -\bottomrule -\endlastfoot - -ADF & Acid detergent fiber (\% of DM) \\ -ADG & Average daily weight gain (g/d) \\ -Age1stBred & First breeding age (month) \\ -BCS5 & Body condition score (1–5 basis) \\ -BW & Body weight (kg) \\ -Ca & Calcium content (\% of DM) \\ -CBW & Calf birth weight (kg) \\ -CI & Calving interval (d) \\ -cm & centimeter \\ -Cost & Feed cost (\$/kg of DM) \\ -CP & Crude protein (\% of DM) \\ -d & days \\ -DE & Digestible energy (standard value, Mcal/kg) \\ -DIM & Days in milk \\ -DM & Dry matter (\% of as-fed basis) \\ -DMI & Dry matter intake \\ -DOP & Days of pregnancy (d) \\ -dRUP & RUP degradability (\% of RUP) \\ -EE & Ether extract, in crude fat (\% DM) \\ -EndCP & Endogenous CP \\ -EndN & Endogenous N \\ -EQSBW & Equivalent shrunk body weight (kg) \\ -FA & Fatty acids \\ -FIPS & Federal Information Processing Standards \\ -g & grams \\ -GE & Gross energy (standard value, Mcal/kg) \\ -GrUterW & Gravid uterine weight (kg) \\ -Kd & Rumen protein degradation rate (\%/h) \\ -kg & kilograms \\ -kJ & kilojoule \\ -L & liters \\ -m & meter \\ -max & maximum \\ -Mcal & Megacalorie \\ -MCP & Microbial Crude Protein \\ -ME & Metabolizable energy (standard value, Mcal/kg) \\ -MICP & Microbial CP \\ -min & minimum \\ -mL & milliliters \\ -MN & Microbial N \\ -MP & Metabolizable protein \\ -MTP & Microbial TP \\ -MW & Mature body weight (kg) \\ -MY & Milk yield \\ -N & Nitrogen (\% of DM) \\ -NASEM & National Academies of Sciences, Engineering, and Medicine \\ -NDF & Neutral detergent fiber (\% of DM) \\ -NEG & Net energy for growth (standard value, Mcal/kg) \\ -NEL & Net energy for lactation (standard value, Mcal/kg) \\ -NEM & Net energy for maintenance (standard value, Mcal/kg) \\ -nNDF & Nondigestible Neutral Detergent Fiber \\ -NPN & Non-protein Nitrogen \\ -NRC & National Research Council (updated in 2021 to NASEM) \\ -OM & Organic matter (\% of DM) \\ -P & Phosphorus content (\% of DM) \\ -PAF & Processing adjustment factor (not used) \\ -Parity & Number of lactations \\ -PrevTemp & Average daily temperature of last month (°C) \\ -RDP & Ruminally degraded CP \\ -ROM & Residual OM (\% of DM) \\ -RUP & Ruminally undegraded CP \\ -s & seconds \\ -TAN & Total ammoniacal N \\ -TDN & Total digestible nutrient (\% of DM) \\ -TP & True protein (\% of DM) \\ -USDA & United States Department of Agriculture \\ -UterW & Uterine weight (kg) \\ -WSC & Water Soluble Carbohydrates \\ -\end{longtable} - \newpage @@ -5339,4 +5025,3 @@ \section{References} \label{sec:References for Manure Module} \printbibliography[heading=subbibliography,title={}] \end{refsection} -\end{document} \ No newline at end of file diff --git a/docs/scientific/manuremoddoc.aux b/docs/scientific/manuremoddoc.aux new file mode 100644 index 0000000000..e6c4eec67f --- /dev/null +++ b/docs/scientific/manuremoddoc.aux @@ -0,0 +1,252 @@ +\relax +\providecommand\babel@aux[2]{} +\@nameuse{bbl@beforestart} +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\catcode 95\active +\abx@aux@refcontext{nyt/global//global/global} +\@writefile{toc}{\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{}} +\babel@aux{english}{} +\@input{manure.aux} +\abx@aux@refsection{1}{6} +\abx@aux@cite{1}{gomez2010time} +\abx@aux@segm{1}{0}{gomez2010time} +\abx@aux@cite{1}{espejo2007herd} +\abx@aux@segm{1}{0}{espejo2007herd} +\abx@aux@cite{1}{jewell2019prevalence} +\abx@aux@segm{1}{0}{jewell2019prevalence} +\abx@aux@cite{1}{meyer2019contract} +\abx@aux@segm{1}{0}{meyer2019contract} +\abx@aux@cite{1}{meyer2019contract} +\abx@aux@segm{1}{0}{meyer2019contract} +\abx@aux@cite{1}{endres2007behavior} +\abx@aux@segm{1}{0}{endres2007behavior} +\abx@aux@cite{1}{gomez2010time} +\abx@aux@segm{1}{0}{gomez2010time} +\abx@aux@cite{1}{Bucklin2009} +\abx@aux@segm{1}{0}{Bucklin2009} +\abx@aux@page{1}{21} +\abx@aux@cite{1}{Rotz2023} +\abx@aux@segm{1}{0}{Rotz2023} +\abx@aux@cite{1}{Chianese2009a} +\abx@aux@segm{1}{0}{Chianese2009a} +\abx@aux@page{2}{22} +\abx@aux@page{3}{22} +\abx@aux@cite{1}{Rotz2006} 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ismn + + + gender + + + + + + + resources/animal.bib + + + + + + resources/animal.bib + + + gomez2010time + espejo2007herd + jewell2019prevalence + meyer2019contract + meyer2019contract + endres2007behavior + gomez2010time + Bucklin2009 + Rotz2023 + Chianese2009a + Rotz2006 + Rotz2006 + Hegg1981 + Mukhtar1999 + Varma2021 + Jorgensen2009 + Fournel2019 + Fernandez2015 + AguirreVillegas2019 + Hanson2024 + Sommer2004 + Sommer2004 + Elsgaard2016 + Petersen2024 + Petersen2024 + Elsgaard2016 + wallaceDMI + Petersen2024 + Petersen2024 + Petersen2024 + Rotz2006 + Rotz2023 + IPCC2019 + IPCC2006 + NRCS2017 + Sommer2004 + Sommer2022 + Elsgaard2016 + Petersen2024 + Petersen2024 + Elsgaard2016 + Petersen2024 + Petersen2024 + Petersen2024 + Rotz2006 + Rotz2023 + IPCC2019 + Hanson2024 + bonifacio2017a + bonifacio2017b + larney2011 + Hanson2024 + Rotz2023 + IPCC2006 + bonifacio2017a + bonifacio2017b + larney2011 + Hanson2024 + Hanson2024 + Hanson2024 + Hanson2024 + bonifacio2017a + bonifacio2017b + larney2011 + Hanson2024 + Hanson2024 + Hanson2024 + Petersen2024 + + + + + + + + presort + + + sortkey + + + sortname + author + editor + translator + sorttitle + title + + + sortyear + year + + + sorttitle + title + + + volume + 0 + + + + + + diff --git a/docs/scientific/manuremoddoc.blg b/docs/scientific/manuremoddoc.blg new file mode 100644 index 0000000000..25d29759ba --- /dev/null +++ b/docs/scientific/manuremoddoc.blg @@ -0,0 +1,24 @@ +[0] Config.pm:307> INFO - This is Biber 2.19 +[0] Config.pm:310> INFO - Logfile is 'manuremoddoc.blg' +[145] biber-MSWIN64:340> INFO - === +[189] Biber.pm:419> INFO - Reading 'manuremoddoc.bcf' +[316] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[320] Biber.pm:979> INFO - Found 28 citekeys in bib section 1 +[320] Biber.pm:979> INFO - Found 0 citekeys in bib section 0 +[343] Biber.pm:4419> INFO - Processing section 1 +[357] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1 +[408] bibtex.pm:1713> INFO - LaTeX decoding ... +[511] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib' +[702] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' +[702] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' +[702] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' +[702] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' +[740] bbl.pm:660> INFO - Writing 'manuremoddoc.bbl' with encoding 'UTF-8' +[764] bbl.pm:763> INFO - Output to manuremoddoc.bbl +[766] Biber.pm:131> WARN - I didn't find a database entry for 'gomez2010time' (section 1) +[766] Biber.pm:131> WARN - I didn't find a database entry for 'espejo2007herd' (section 1) +[766] Biber.pm:131> WARN - I didn't find a database entry for 'jewell2019prevalence' (section 1) +[766] Biber.pm:131> WARN - I didn't find a database entry for 'meyer2019contract' (section 1) +[766] Biber.pm:131> WARN - I didn't find a database entry for 'endres2007behavior' (section 1) +[766] Biber.pm:131> WARN - I didn't find a database entry for 'wallaceDMI' (section 1) +[766] Biber.pm:133> INFO - WARNINGS: 6 diff --git a/docs/scientific/manuremoddoc.fdb_latexmk b/docs/scientific/manuremoddoc.fdb_latexmk new file mode 100644 index 0000000000..17fe9489de --- /dev/null +++ b/docs/scientific/manuremoddoc.fdb_latexmk @@ -0,0 +1,293 @@ +# Fdb version 4 +["biber manuremoddoc"] 1772660324.47158 "manuremoddoc.bcf" "manuremoddoc.bbl" "manuremoddoc" 1772717093.40978 0 + "manuremoddoc.bcf" 1772717092 112612 b8a1d99bc249c8ada58fb65f4341bbe0 "pdflatex" + "resources/animal.bib" 1772218264 19843 003ce6dc3163a9c1fd885dbc082d404e "" + (generated) + "manuremoddoc.bbl" + "manuremoddoc.blg" + (rewritten before read) +["pdflatex"] 1772717087.05468 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/manuremoddoc.tex" "manuremoddoc.pdf" 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C:\Users\gmg228\AppData\Local\Programs\MiKTeX\fonts\type1\public\amsfonts\cm\cmsy5.pfb +INPUT C:\Users\gmg228\AppData\Local\Programs\MiKTeX\fonts\type1\public\amsfonts\cm\cmsy5.pfb +INPUT C:\Users\gmg228\AppData\Local\Programs\MiKTeX\fonts\type1\public\amsfonts\cm\cmsy7.pfb +INPUT C:\Users\gmg228\AppData\Local\Programs\MiKTeX\fonts\type1\public\amsfonts\cm\cmsy7.pfb diff --git a/docs/scientific/manuremoddoc.lof b/docs/scientific/manuremoddoc.lof new file mode 100644 index 0000000000..3623bc9599 --- /dev/null +++ b/docs/scientific/manuremoddoc.lof @@ -0,0 +1,5 @@ +\babel@toc {english}{}\relax +\contentsline {figure}{\numberline {1}{\ignorespaces A real-world example of a simplistic manure management chain. }}{7}{figure.caption.2}% +\contentsline {figure}{\numberline {2}{\ignorespaces The manure management chain illustrated in the previous figure, with RuFaS-specific information reflected. }}{7}{figure.caption.3}% +\contentsline {figure}{\numberline {3}{\ignorespaces If manure from a pen is routed to two different general manure streams, two sets of manure stream inputs must be defined. An example of a single pen’s manure stream inputs is above - in this example, manure from this pen is routed to two locations, one representing an exercise lot, the other representing a bedded pack area.}}{13}{figure.caption.5}% +\contentsline {figure}{\numberline {4}{\ignorespaces \relax }}{95}{figure.caption.35}% diff --git a/docs/scientific/manuremoddoc.lot b/docs/scientific/manuremoddoc.lot new file mode 100644 index 0000000000..60865f3849 --- /dev/null +++ b/docs/scientific/manuremoddoc.lot @@ -0,0 +1,40 @@ +\babel@toc {english}{}\relax +\contentsline {table}{\numberline {1}{\ignorespaces Examples of processor types by class.}}{6}{table.caption.1}% +\contentsline {table}{\numberline {2}{\ignorespaces List of Python classes for Animal to Manure Module connection.}}{9}{table.caption.4}% +\contentsline {table}{\numberline {3}{\ignorespaces User inputs for Stream Formation and Bedding sections.}}{10}{table.3}% +\contentsline {table}{\numberline {4}{\ignorespaces Recommended minutes\_away\_for\_milking by pen type based on published literature. Remember, this does not necessarily reflect the model defaults. }}{15}{table.caption.6}% +\contentsline {table}{\numberline {5}{\ignorespaces Proportions of differnt streams for different animal classes.}}{15}{table.caption.7}% +\contentsline {table}{\numberline {6}{\ignorespaces Calculated manure and bedding characteristics}}{17}{table.caption.8}% +\contentsline {table}{\numberline {7}{\ignorespaces The classes of handlers that are used in this module.}}{19}{table.caption.9}% +\contentsline {table}{\numberline {8}{\ignorespaces Required inputs for the Manure Handler (refreshed\_manure\_management.json)}}{19}{table.caption.10}% +\contentsline {table}{\numberline {9}{\ignorespaces The surface area per stall that is covered with manure is a function of the pen type and type of animal housed.}}{23}{table.caption.11}% +\contentsline {table}{\numberline {10}{\ignorespaces Calculated manure storage variables and their units}}{26}{table.caption.12}% +\contentsline {table}{\numberline {11}{\ignorespaces List of Python classes for solid liquid separators.}}{27}{table.caption.13}% +\contentsline {table}{\numberline {12}{\ignorespaces The required inputs of this section.}}{27}{table.12}% +\contentsline {table}{\numberline {13}{\ignorespaces The default, minimums, and maximums for various separation efficiencies.}}{30}{table.caption.14}% +\contentsline {table}{\numberline {14}{\ignorespaces Solids and liquid fraction calculations for separated manure components}}{31}{table.14}% +\contentsline {table}{\numberline {15}{\ignorespaces List of Python classes for anaerobic digestors.}}{34}{table.caption.15}% +\contentsline {table}{\numberline {16}{\ignorespaces Required inputs for this section.}}{34}{table.caption.16}% +\contentsline {table}{\numberline {17}{\ignorespaces Calculated anaerobic digestion outputs.}}{40}{table.17}% +\contentsline {table}{\numberline {18}{\ignorespaces Key differences for two options of slurry storage.}}{41}{table.caption.17}% +\contentsline {table}{\numberline {19}{\ignorespaces Required inputs for the slurry storage section.}}{42}{table.caption.19}% +\contentsline {table}{\numberline {20}{\ignorespaces Manure storage variable calculations}}{50}{table.20}% +\contentsline {table}{\numberline {21}{\ignorespaces List of Python classes for anaerobic lagoon.}}{52}{table.caption.20}% +\contentsline {table}{\numberline {22}{\ignorespaces Required inputs for the anaerobic lagoon section (refreshed\_manure\_management.json)}}{52}{table.caption.21}% +\contentsline {table}{\numberline {23}{\ignorespaces Manure storage variable calculations}}{61}{table.23}% +\contentsline {table}{\numberline {24}{\ignorespaces List of classes for bedded pack.}}{63}{table.caption.22}% +\contentsline {table}{\numberline {25}{\ignorespaces Required inputs for the bedded pack section (refreshed\_manure\_management.json)}}{63}{table.caption.23}% +\contentsline {table}{\numberline {26}{\ignorespaces Methane conversion factor values for bedded pack pens, based on presence or absence of mixing and average annual air temperature.}}{64}{table.caption.24}% +\contentsline {table}{\numberline {27}{\ignorespaces Calculated manure storage variables and their units}}{70}{table.27}% +\contentsline {table}{\numberline {28}{\ignorespaces Classes available in open lots.}}{73}{table.caption.25}% +\contentsline {table}{\numberline {29}{\ignorespaces Required inputs for the open lots section}}{73}{table.caption.26}% +\contentsline {table}{\numberline {30}{\ignorespaces Calculated manure storage variables and their units}}{80}{table.30}% +\contentsline {table}{\numberline {31}{\ignorespaces Classes available in composting.}}{82}{table.caption.27}% +\contentsline {table}{\numberline {32}{\ignorespaces Required inputs for the composting section (refreshed\_manure\_management.json)}}{83}{table.caption.28}% +\contentsline {table}{\numberline {33}{\ignorespaces Methane conversion factor values for compost pens, based on composting method and average annual air temperature.}}{84}{table.caption.29}% +\contentsline {table}{\numberline {34}{\ignorespaces NH\textsubscript {3}-N emission factors for compost by composting method.}}{88}{table.caption.30}% +\contentsline {table}{\numberline {35}{\ignorespaces N\textsubscript {2}O-N emission factors for compost by composting method.}}{89}{table.caption.32}% +\contentsline {table}{\numberline {36}{\ignorespaces Manure storage variable calculations}}{90}{table.36}% +\contentsline {table}{\numberline {37}{\ignorespaces List of classes for daily spread.}}{92}{table.caption.33}% +\contentsline {table}{\numberline {38}{\ignorespaces Required inputs for the daily spread section (refreshed\_manure\_management.json)}}{92}{table.caption.34}% +\contentsline {table}{\numberline {39}{\ignorespaces The key constants for all equations in the Manure Module}}{98}{table.39}% diff --git a/docs/scientific/manuremoddoc.out b/docs/scientific/manuremoddoc.out new file mode 100644 index 0000000000..4b82de6206 --- 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b/docs/scientific/manuremoddoc.run.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + +]> + + + latex + + manuremoddoc.bcf + + + manuremoddoc.bbl + + + blx-dm.def + blx-compat.def + biblatex.def + blx-natbib.def + standard.bbx + authoryear.bbx + authoryear.cbx + biblatex.cfg + english.lbx + + + + biber + + biber + manuremoddoc + + + manuremoddoc.bcf + + + manuremoddoc.bbl + + + manuremoddoc.bbl + + + manuremoddoc.bcf + + + resources/animal.bib + + + diff --git a/docs/scientific/manuremoddoc.synctex.gz b/docs/scientific/manuremoddoc.synctex.gz new file mode 100644 index 0000000000..b0e8f7ebd4 Binary files /dev/null and b/docs/scientific/manuremoddoc.synctex.gz differ diff --git a/docs/scientific/manuremoddoc.tex b/docs/scientific/manuremoddoc.tex new file mode 100644 index 0000000000..f55032ee39 --- /dev/null +++ b/docs/scientific/manuremoddoc.tex @@ -0,0 +1,33 @@ +\documentclass{article} + +\input{preamble} + +\begin{document} + + + \thispagestyle{empty} + \centering + \vspace*{2cm} + + {\Huge\bfseries Manure Module\par} + \vspace{1cm} + + {\Large RuFaS Scientific Documentation\par} + \vspace{1cm} + + \includegraphics[width=0.5\textwidth]{resources/manure.png} % Adjust size and filename + + \vfill + + {\small v.1\par} + \vspace*{1cm} + +\newpage + + +% Continue with front matter (e.g., table of contents) +\thispagestyle{fancy} % Ensure the header/footer appears on the first page + +\include{manure} + +\end{document} \ No newline at end of file diff --git a/docs/scientific/manuremoddoc.toc b/docs/scientific/manuremoddoc.toc new file mode 100644 index 0000000000..c8539ec947 --- /dev/null +++ b/docs/scientific/manuremoddoc.toc @@ -0,0 +1,56 @@ +\@ifundefined {etoctocstyle}{\let \etoc@startlocaltoc \@gobble \let \etoc@settocdepth \@gobble \let \etoc@depthtag \@gobble \let \etoc@setlocaltop \@gobble }{} +\babel@toc {english}{}\relax +\contentsline {part}{I\hspace {1em}Manure Module}{2}{part.1}% +\etoc@startlocaltoc {1} +\contentsline {section}{\numberline {I.}Module Introduction}{6}{section.1}% +\contentsline {subsection}{\numberline {A.}Structural setup of the Manure Module}{6}{subsection.1.1}% +\contentsline {subsection}{\numberline {B.}Overview of Required Inputs}{7}{subsection.1.2}% +\contentsline {subsection}{\numberline {C.}General Assumptions of the Manure Module}{8}{subsection.1.3}% +\contentsline {section}{\numberline {II.}Animal and Manure Module Connection}{9}{section.2}% +\contentsline {subsection}{\numberline {A.}Introduction}{9}{subsection.2.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{12}{subsection.2.2}% +\contentsline {section}{\numberline {III.}Manure Handler}{17}{section.3}% +\contentsline {subsection}{\numberline {A.}Introduction}{17}{subsection.3.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{21}{subsection.3.2}% +\contentsline {subsection}{\numberline {C.}Manure composition update}{26}{subsection.3.3}% +\contentsline {section}{\numberline {IV.}Solid Liquid Separators}{26}{section.4}% +\contentsline {subsection}{\numberline {A.}Introduction}{26}{subsection.4.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{29}{subsection.4.2}% +\contentsline {subsection}{\numberline {C.}Manure composition update}{31}{subsection.4.3}% +\contentsline {section}{\numberline {V.}Anaerobic Digestion}{33}{section.5}% +\contentsline {subsection}{\numberline {A.}Introduction}{33}{subsection.5.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{35}{subsection.5.2}% +\contentsline {subsection}{\numberline {C.}Manure composition update}{39}{subsection.5.3}% +\contentsline {section}{\numberline {VI.}Slurry Storage}{41}{section.6}% +\contentsline {subsection}{\numberline {A.}Introduction}{41}{subsection.6.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{43}{subsection.6.2}% +\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{49}{subsection.6.3}% +\contentsline {subsection}{\numberline {D.}Manure composition updates}{50}{subsection.6.4}% +\contentsline {section}{\numberline {VII.}Anaerobic Lagoon}{51}{section.7}% +\contentsline {subsection}{\numberline {A.}Introduction}{51}{subsection.7.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{53}{subsection.7.2}% +\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{60}{subsection.7.3}% +\contentsline {subsection}{\numberline {D.}Manure composition updates}{60}{subsection.7.4}% +\contentsline {section}{\numberline {VIII.}Bedded Pack}{62}{section.8}% +\contentsline {subsection}{\numberline {A.}Introduction}{62}{subsection.8.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{64}{subsection.8.2}% +\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{69}{subsection.8.3}% +\contentsline {subsection}{\numberline {D.}Manure composition updates}{70}{subsection.8.4}% +\contentsline {section}{\numberline {IX.}Open Lot}{72}{section.9}% +\contentsline {subsection}{\numberline {A.}Introduction}{72}{subsection.9.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{74}{subsection.9.2}% +\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{79}{subsection.9.3}% +\contentsline {subsection}{\numberline {D.}Manure composition updates}{80}{subsection.9.4}% +\contentsline {section}{\numberline {X.}Composting}{82}{section.10}% +\contentsline {subsection}{\numberline {A.}Introduction}{82}{subsection.10.1}% +\contentsline {subsection}{\numberline {B.}Methodology}{84}{subsection.10.2}% +\contentsline {subsection}{\numberline {C.}Received, stored, and emptied outputs}{89}{subsection.10.3}% +\contentsline {subsection}{\numberline {D.}Manure composition updates}{90}{subsection.10.4}% +\contentsline {section}{\numberline {XI.}Daily spread}{92}{section.11}% +\contentsline {subsection}{\numberline {A.}Introduction}{92}{subsection.11.1}% +\contentsline {section}{\numberline {XII.}Manure to Soil and Crop Module Connection}{94}{section.12}% +\contentsline {subsection}{\numberline {A.}Introduction}{94}{subsection.12.1}% +\contentsline {subsection}{\numberline {B.}Implementation in RuFaS}{94}{subsection.12.2}% +\contentsline {subsection}{\numberline {C.}Methodology}{95}{subsection.12.3}% +\contentsline {section}{\numberline {XIII.}Key Constants}{98}{section.13}% +\contentsline {section}{\numberline {XIV.}References}{101}{section.14}% diff --git a/docs/scientific/preamble.aux b/docs/scientific/preamble.aux new file mode 100644 index 0000000000..b64012178f --- /dev/null +++ b/docs/scientific/preamble.aux @@ -0,0 +1,2 @@ +\relax +\gdef \@abspage@last{1} diff --git a/docs/scientific/preamble.bbl b/docs/scientific/preamble.bbl new file mode 100644 index 0000000000..005f3858be --- /dev/null +++ b/docs/scientific/preamble.bbl @@ -0,0 +1,20 @@ +% $ biblatex auxiliary file $ +% $ biblatex bbl format version 3.2 $ +% Do not modify the above lines! +% +% This is an auxiliary file used by the 'biblatex' package. +% This file may safely be deleted. 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