Getting Started with MacroIBI

Overview

MacroIBI is an R/Shiny application for calculating a macroinvertebrate-based Index of Biotic Integrity (IBI) for wetlands using the MPCA protocol. The package provides an interactive dashboard for data entry, metric calculation, and report generation.

Try before installing: A demo version is available at https://smsc2.shinyapps.io/MacroIBI/ (some features disabled). Install locally for full functionality.

Installation

Requirements

R 4.2.0 or newer — Download from https://cran.r-project.org
RStudio (recommended) — Download from https://posit.co/download/rstudio-desktop/
Rtools (Windows only) — Download from https://cran.r-project.org/bin/windows/Rtools/
LaTeX (optional, for PDF exports) — Install TinyTeX after MacroIBI:
```
install.packages("tinytex")
tinytex::install_tinytex()
```
Chrome or Chromium (optional, for PNG table image export)

If you are new to R, see vignette("field-and-app-guide", package = "macroibi") for detailed step-by-step installation instructions with troubleshooting tips.

Install MacroIBI

install.packages("remotes")
remotes::install_github("aomop/MacroIBI")

Launching the App

library(macroibi)
run_macroibi()

A browser window will open with the Wetland IBI Dashboard.

Basic Workflow

1. Enter metadata

When the app opens, enter a sample title and date, then click Let’s go!. You can also skip metadata if you plan to upload data or reload an autosave.

2. Enable autosave

On the Data tab, find Autosave Settings on the left sidebar and enable auto-save. This periodically saves your progress and allows recovery after crashes. Data Summary and Full Report exports rely on autosave history.

3. Enter taxa and counts

Use Select Taxon to search and add taxa. The app assigns each taxon to the correct group automatically. Each row shows:

Taxon name
Dipnet 1 count
Dipnet 2 count
Sum count (auto-calculated)

Group footers update live with total taxa, percent of total sample, and total individuals.

4. Review metrics

Switch to the Results tab to see real-time IBI calculations:

Total individuals
EOT richness (Ephemeroptera, Odonata, Trichoptera)
Snail richness
All-taxa richness
Corixid ratio
Abundance of EOT
Overall IBI score (0–50)

Hover over “How are these calculated?” for metric formulas.

5. Export results

Data tab sidebar:

Raw Data CSV — for archiving or re-uploading into the app

Results tab:

Results CSV — final calculated metric scores
Table Image (PNG) — formatted metric table (requires Chrome)
Data Summary (PDF) — concise one-page snapshot (requires LaTeX)
Full Report (PDF) — comprehensive report with comparisons to other autosaved sessions (requires LaTeX)

Demo Mode

To explore the app with bundled sample data (no files are written to disk):

run_macroibi(demo_mode = TRUE)

Click “OK” on the demo message, then click Load Autosave on the left sidebar. Demo files will be listed so you can explore all features.

Batch Export

For scripted or automated workflows, use generate_reports() to produce outputs without launching the Shiny app. See vignette("batch-export", package = "macroibi") for details.

Where Are My Files Saved?

Autosaves are stored in your user data folder:

Windows: C:\Users\[YourName]\AppData\Local\R\macroibi\data\
Mac: ~/Library/Application Support/macroibi/data/