MacroIBI

A Shiny application for calculating a macroinvertebrate-based Index of Biotic Integrity (IBI) for wetlands, packaged for easy installation.

Please see the FIELD AND APP GUIDE for questions about sampling protocol or how to use the app

A demo version of the app is available to preview at https://smsc2.shinyapps.io/MacroIBI/. Install the package locally to access all features.

Prerequisites and quickstart

• Supported R: 4.2.0 or newer
• Key packages installed automatically: shiny, bslib, DT, webshot2, dplyr, readr, rmarkdown, ggplot2, and other listed Imports in DESCRIPTION
• Quick start:

  if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
  remotes::install_github("aomop/MacroIBI")   # install
  library(macroibi)
  run_macroibi()                              # launch the app
  tools::R_user_dir("macroibi", "data")      # view autosave folder used by the app

Installation

Ensure R and RStudio are installed, then run:

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("aomop/MacroIBI")

Running the App

From the console, run:

library(macroibi)
run_macroibi()

The app bundles its static assets and taxonomy reference data inside the package. Autosave files are written to a per-user data directory obtained via tools::R_user_dir("macroibi", "data").

Key Features

• Interactive taxon entry by group with inline counts, dynamic summaries, and optional taxonomic hierarchy view
• Built-in metrics module computes EOT taxa, snail taxa, corixid ratio, abundance of EOT, and overall IBI score
• Optional auto-save that periodically writes taxa and metric data to a user-specific cache and reloads saved datasets
• Import previously saved CSV data to repopulate taxon tables
• Export results as CSV, PNG table image, and PDF reports
• Visualize selected taxa as an annotated phylogenetic tree
• Raw/Imported CSV scope: The exported Raw Data CSV is intended only for datasets created within MacroIBI. Avoid modifying it externally or feeding unrelated/prepared data from other systems back into the app.

Project Structure

• R/ – package functions, modules, and app entry point
• inst/app/www/ – bundled assets (templates, styles, images)
• inst/extdata/ – bundled taxonomy data
• tests/testthat/ – smoke tests for the package entry point

Testing

devtools::test()

Support & contributions

• Questions and issues: Please open an issue at https://github.com/aomop/MacroIBI/issues. We aim to respond within 5 business days.
• Contributions: Fork the repo, open a pull request with a concise description of the change, and include any relevant testing notes. Bug fixes and documentation improvements are welcome.

License

This project is licensed under the MIT License.