Organize voucher directories

This guide demonstrates how to use the mk_voucher_dirs function in the forplotR package to create and organize image directories of vouchers recorded in plot censuses based on their updated taxonomic identification.

Function Overview

The mk_voucher_dirs() function organizes voucher image folders according to the most up-to-date taxonomic identification found in a ForestPlots-style Excel file.

It is safe to run multiple times:

First run: creates the main output folder (default: "voucher_imgs") and, for each voucher marked as Collected, creates the directory structure Family/Genus/Voucher.
Subsequent runs (reorganization): detects vouchers placed under outdated genera and moves images to the correct folder without overwriting existing files; then removes empty, outdated directories.

Basic Use Case

mk_voucher_dirs(
  fp_file_path = "data/RUS_plot.xlsx",
  output_dir   = "voucher_imgs"
)

Reorganizing After Taxonomic Updates

If some vouchers were reidentified (e.g., genus changed), just run the function again:

mk_voucher_dirs(
  fp_file_path = "data/RUS_plot.xlsx",
  output_dir   = "voucher_imgs"
)

Images found under an outdated genus folder are moved to the correct genus folder.
The function does not overwrite existing files in the correct destination.
Any empty old voucher folders are removed.

Using a Custom Output Directory

mk_voucher_dirs(
  fp_file_path = "data/Inventory_A.xlsx",
  output_dir   = "parcelA_voucher_imgs"
)

Inspecting the Resulting Structure

# List created directories (first levels)
list.dirs("voucher_imgs", recursive = FALSE)

# Inspect all voucher-level directories
dirs <- list.dirs("voucher_imgs", recursive = TRUE, full.names = TRUE)
head(dirs, 20)

Run mk_voucher_dirs() first to create voucher_imgs

Tips

Ensure your Excel file includes columns like Family, Original determination, Voucher, and Collected.
The genus is derived from the first token in Original determination (text before the first space).
Re-run the function whenever identifications change; it is designed to be idempotent.
Consider keeping a backup before large reorganizations when working with many images.
If a destination folder already has images, the function skips moving to avoid overwriting—review manually if you want to merge.

--- title: "Organize voucher directories" format: html execute: echo: false eval: true freeze: auto cache: false warning: false message: false include: true inline: true --- ```{r setup, include=FALSE} library(forplotR) ``` This guide demonstrates how to use the `mk_voucher_dirs` function in the `forplotR` package to create and organize image directories of vouchers recorded in plot censuses based on their **updated taxonomic identification**. ## Function Overview The `mk_voucher_dirs()` function organizes **voucher image folders** according to the most up-to-date taxonomic identification found in a **ForestPlots-style** Excel file. It is safe to run multiple times: * **First run:** creates the main output folder (default: `"voucher_imgs"`) and, for each voucher marked as **Collected**, creates the directory structure `Family/Genus/Voucher`. * **Subsequent runs (reorganization):** detects vouchers placed under outdated genera and **moves images** to the correct folder **without overwriting** existing files; then **removes empty, outdated directories**. ## Basic Use Case ```r mk_voucher_dirs( fp_file_path = "data/RUS_plot.xlsx", output_dir = "voucher_imgs" ) ``` ## Reorganizing After Taxonomic Updates If some vouchers were reidentified (e.g., genus changed), just run the function again: ```r mk_voucher_dirs( fp_file_path = "data/RUS_plot.xlsx", output_dir = "voucher_imgs" ) ``` * Images found under an outdated genus folder are **moved** to the correct genus folder. * The function **does not overwrite** existing files in the correct destination. * Any **empty old voucher folders** are removed. ## Using a Custom Output Directory ```r mk_voucher_dirs( fp_file_path = "data/Inventory_A.xlsx", output_dir = "parcelA_voucher_imgs" ) ``` ## Inspecting the Resulting Structure ```r # List created directories (first levels) list.dirs("voucher_imgs", recursive = FALSE) # Inspect all voucher-level directories dirs <- list.dirs("voucher_imgs", recursive = TRUE, full.names = TRUE) head(dirs, 20) ``` ```{r} #| echo: false # Quick check: count voucher directories under output_dir out <- "voucher_imgs" if (dir.exists(out)) { all_dirs <- list.dirs(out, recursive = TRUE, full.names = TRUE) voucher_dirs <- all_dirs[grepl("[A-Za-z]+/[A-Za-z]+/[A-Za-z]{2,}[0-9]{3,}", all_dirs)] cat("Total voucher directories found:", length(voucher_dirs), " ") } else { cat("Run mk_voucher_dirs() first to create", out, " ") } ``` ## Tips * Ensure your Excel file includes columns like `Family`, `Original determination`, `Voucher`, and `Collected`. * The **genus** is derived from the **first token** in `Original determination` (text before the first space). * Re-run the function whenever identifications change; it is designed to be **idempotent**. * Consider keeping a **backup** before large reorganizations when working with many images. * If a destination folder already has images, the function **skips moving** to avoid overwriting—review manually if you want to merge.