Batch Report Generation • macroibi

Overview

generate_reports() lets you produce IBI outputs from autosave files without launching the Shiny app. This is useful for scripted workflows, scheduled report generation, and automation pipelines.

Prerequisites

Autosave files must already exist from previous interactive sessions. By default, the function looks for autosaves in the package’s user data directory:

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

Basic Usage

Generate all output types for all autosave files:

library(macroibi)
generate_reports()

This creates metric CSVs, raw data CSVs, PDF reports, and PDF summaries in your current working directory.

Output Types

The output_type parameter controls which outputs to generate:

Value	Description
`"metrics"`	Metric scores as CSV
`"raw_data"`	Raw taxa data as CSV
`"pdf_report"`	Full PDF report with comparisons
`"pdf_summary"`	Concise data summary PDF
`"all"`	All of the above (default)

# Only metric CSVs
generate_reports(output_type = "metrics")

# Only PDF reports
generate_reports(output_type = "pdf_report")

Processing Specific Files

By default, all autosave files are processed. To target a specific file, pass its filename:

generate_reports(
  autosave_file = "autosave_MyWetland.rds",
  output_type = "pdf_report",
  output_path = "~/reports"
)

Custom Output Directory

Use output_path to control where files are written. The directory is created automatically if it does not exist:

generate_reports(output_path = "~/wetland_exports/2025")

Custom Autosave Directory

If your autosave files are in a non-default location, use autosave_path:

generate_reports(
  autosave_path = "/shared/macroibi_data",
  output_path = "~/reports"
)

Return Value

generate_reports() invisibly returns a data frame summarizing the results:

Column	Description
`autosave_file`	Name of the processed autosave file
`output_type`	Type of output generated
`output_file`	Path to the generated file
`success`	Logical indicating success
`message`	Status or error message

results <- generate_reports(output_type = "metrics")
print(results)

Integration with Automated Pipelines

R script for scheduled runs

#!/usr/bin/env Rscript
library(macroibi)

results <- generate_reports(
  output_type = "all",
  output_path = "/output/macroibi"
)

failures <- results[!results$success, ]
if (nrow(failures) > 0) {
  warning("Some reports failed:\n", paste(failures$message, collapse = "\n"))
}

Command-line invocation

You can call the above script from a shell or scheduler:

Rscript generate_all_reports.R

This makes it straightforward to integrate MacroIBI report generation into cron jobs, Task Scheduler, or CI/CD workflows.