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.
• Contributions: Fork the repo, open a pull request with a concise description of the change, and include any relevant testing notes. Find more details in the contributing guidelines.
• Security: I cannot fathom what security issues may arise from use of this app, but if you find one, please follow the steps outlined in the security document.

License

This project is licensed under the MIT License.