Update pkg infra for init rename

Author: pratikunterwegs

.Rbuildignore

@@ -13,3 +13,4 @@
 ^docs$
 ^pkgdown$
 ^tools$
+^scratch\.R$

.gitignore

@@ -49,3 +49,4 @@ po/*~
 rsconnect/
 inst/doc
 docs
+scratch.R

.lintr

@@ -1,6 +1,5 @@
 linters: all_linters(
     indentation_linter = NULL, # unstable as of lintr 3.1.0
-    extraction_operator_linter = NULL, # lints auto-generated vignette setup chunks
     implicit_integer_linter = NULL, # turn off due to multiple integerish values used
     duplicate_argument_linter = NULL, # due to cli_bullets
     object_name_linter = NULL, # due to S3 methods
@@ -20,8 +19,5 @@ exclusions: list(
     ),
     "vignettes" = list(
       undesirable_function_linter = Inf
-    ),
-    # do no attempt to lint auto-generated files
-    "R/RcppExports.R",
-    "R/cpp11.R"
+    )
   )

DESCRIPTION

@@ -1,15 +1,23 @@
-Package: vimc.rpkg.template
-Title: Your Package Title in Title Case
+Package: vimcheck
+Title: Diagnostics for Vaccination Modelling Burden and Impact Estimates
 Version: 0.0.0.9000
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),
+    person("Katy", "Gaythorpe", role = "aut",
+           comment = c(ORCID = "0000-0003-3734-9081")),
+    person("Xiang", "Li", role = "aut",
+           comment = c(ORCID = "0000-0002-5945-159X")),
+    person("Zoe", "Gibney", role = "aut"),
     person("Imperial College of Science, Technology and Medicine", role = c("cph", "fnd"))
   )
-Description: Your package description. It must end with a period (".") and
-    include relevant bibliographical references if applicable, using the
-    following format: Author et al. (2023) <doi:10.5281/zenodo.6619350>.
+Description: Run diagnostics on burden estimates submitted to the Vaccine
+    Impact Modelling Consortium (VIMC), and impacts estimated by VIMC, as
+    described in Echeverria-Londono et al.  (2021)
+    <doi:10.1186/s12889-021-12040-9>.
 License: MIT + file LICENSE
+URL: https://github.com/vimc/vimcheck, https://vimc.github.io/vimcheck/
+BugReports: https://github.com/vimc/vimcheck/issues
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -1,3 +1,2 @@
 # Generated by roxygen2: do not edit by hand
 
-export(get_manual_mean)

NEWS.md

@@ -1,5 +1,5 @@
-# vimc.rpkg.template 0.0.1
+# vimcheck 0.0.1
 
-* This project now includes a
-   [`NEWS.md`](https://r-pkgs.org/other-markdown.html#sec-news) file to inform
-   users about changes and new features.
+- Added GHA workflows to notify of changed dependencies, auto-render `README.md` from `README.Rmd`, and update the copyright year annually.
+
+- Added reference to VIMC paper (Echeverria-Londono et al. 2021).

README.Rmd

@@ -1,6 +1,6 @@
 ---
 output: github_document
-# add bibliography here
+bibliography: vignettes/resources/references.json
 link-citations: true
 ---
 
@@ -15,40 +15,25 @@ knitr::opts_chunk$set(
 )
 ```
 
-# vimc.rpkg.template: TAGLINE
+# vimcheck: Diagnostics for vaccination modelling burden and impact estimates
 
 <!-- badges: start -->
 [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
-[![R build status](https://github.com/vimc/vimc.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimc.rpkg.template/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/vimc/vimc.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimc.rpkg.template?branch=main)
-[![CRAN status](https://www.r-pkg.org/badges/version/vimc.rpkg.template)](https://CRAN.R-project.org/package=vimc.rpkg.template)
+[![R build status](https://github.com/vimc/vimcheck/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimcheck/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/vimc/vimcheck/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimcheck?branch=main)
+[![CRAN status](https://www.r-pkg.org/badges/version/vimcheck)](https://CRAN.R-project.org/package=vimcheck)
 <!-- badges: end -->
 
-_vimc.rpkg.template_ is a template package and repository on which future VIMC R packages are based.
-
-To use this template, select _vimc.rpkg.template_ from the drop-down menu under **Repository template** when creating a new repository in the VIMC GitHub organisation.
-Replace all instances of `"vimc.rpkg.template"` with your package name. Make sure to also:
-
-1. Edit the `DESCRIPTION` as appropriate with the correct package information, including authors;
-
-2. Edit the files in `R/`, `tests/`, and `vignettes/` to suit your package;
-
-3. Add spell check by running `usethis::use_spell_check(lang = "en-GB")`;
-
-4. Remove these instructions from `README.Rmd`, and re-render the `.md` file using `devtools::render_readme()`.
+_vimcheck_ is an R package for running diagnostic checks on burden estimates submitted to the Vaccine Impact Modelling Consortium (VIMC), and on impact estimates calculated by VIMC.
 
 ## Installation
 
-**NOTE:** Remove or comment out installation sources as appropriate.
-
-**Remember** to add the package to the [VIMC R-universe](https://github.com/vimc/vimc.r-universe.dev).
-
-You can install the development version of _vimc.rpkg.template_ from the VIMC R-universe with:
+You can install the development version of _vimcheck_ from the VIMC R-universe with:
 
 ```r
 installation from R-universe
 install.packages(
-  "vimc.rpkg.template", 
+  "vimcheck", 
   repos = c(
     "https://vimc.r-universe.dev", "https://cloud.r-project.org"
   )
@@ -59,18 +44,15 @@ or from GitHub [GitHub](https://github.com/) with:
 
 ``` r
 install.packages("pak")
-pak::pak("vimc/vimc.rpkg.template")
+pak::pak("vimc/vimcheck")
 ```
 
 ## Quick start
 
-Add a simple example of using the package's main feature(s) here, with a minimum amount of code.
-If preparatory or plotting steps are needed, prefer to hide them to keep focus on the package functionality.
+WIP.
 
 ## Related projects
 
-Add information and links to related projects, such as research papers or packages, here.
+VIMC impact assessment workflows are described in @echeverria-londono2021.
 
 ## References
-
-Space for references: REMOVE this text.

inst/WORDLIST

@@ -1,9 +1,25 @@
+BMC
 Codecov
+De
+Echeverria
+GHA
+Hallett
+Jaspreet
+Kaja
+Londono
+Modelling
+Nayagam
 ORCID
-TAGLINE
+Shevanthi
+Susy
+Toor
 VIMC
+Villiers
+WIP
+al
 doi
+et
+explainers
+funder
+modelling
 pkgdown
-rpkg
-vimc
-zenodo