Example file structure – Inventory

This is a tidied up version of the file and directory names that power BirdOMatic.  I thought about sharing the actual ones, but we’re still in pretty heavy development/debugging mode and I’ve embedded a lot of versioning crud in them so they’re really messy.  Some day I’ll run through and use these names in the production system.

Click here for the text file that contains the inventory explained below (great for copy/pasting).

Click here for a zip file that you can expand into actual directories and empty files (great for actually building the file structure in one go).

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birdnet_analyzer_RUN_FILES: folder contains yearly destination folders for the BirdNET-Analyzer script, each contains 1 selection.table.txt file per bioacoustic audio file in that year

 birdnet_analyzer_RUN_FILES
   run_files_2020
   run_files_2021
   run_files_2022
   run_files_2023
   run_files_2024
   run_files_2025

birdnet_analyzer_run_files_COMBINED: contains yearly run_files_COMBINED_202n.txt files that are updated throughout the year

birdnet_analyzer_run_files_COMBINED
   run_files_COMBINED_2020.txt
   run_files_COMBINED_2021.txt
   run_files_COMBINED_2022.txt
   run_files_COMBINED_2023.txt
   run_files_COMBINED_2024.txt
   run_files_COMBINED_2025.txt

birdnet_analyzer_run_files_combined_FST:  the destination folder for the combine_birdnet_runs.r  script which creates annual files by year and the all-years run_files_ combined_FST.DateStamp.fst file.  The all-years file is the data table used by the R script that powers the UI.

birdnet_analyzer_run_files_combined_FST
   run_files_combined_FST.2020.fst
   run_files_combined_FST.2021.fst
   run_files_combined_FST.2022.fst
   run_files_combined_FST.2023.fst
   run_files_combined_FST.2024.fst
   run_files_combined_FST.2025.fst
   run_files_combined_DateStamp.fst

BirdWorkbench_BASH_scripts is a folder for the BASH scripts (click some links to learn what they are/do).  Best to check the GitHub site for the latest versions.

BirdWorkbench_BASH_scripts
   BirdNET_run_file_combiner_prod
   maintenance_archive_to_FST_update_test.sh
   maintenance_archive_to_FST_update_prod.sh
   maintenance_PGBWB_nightly.sh

BirdWorkbench_R_scripts is a folder for R scripts (click some links to learn what they are/do).  Best to check the GitHub site for the latest versions.

BirdWorkbench_R_Scripts
   www
   bird-workbench_UI.m20_prod.R
   bird-workbench_UI.m20_test.R
   combine_birdnet_runs_2025_prod.R
   tiny_shiny.R

weather_snoop_valley_weather:  a place for a copy of the weather database valley.weather.db  file.  This database is accessed by the combine_birdnet_runs_yyyy.r script to add weather (temp and wind-speed) data to each row of the .FST file.  You’ll either want to delete that section from the R script, or come up with your own weather database and stitch it in.

weather_snoop_valley_weather
	valley.weather.db

Bioacoustic Archive:  the archive is running on an external RAID disk array and the data is arranged in yearly directories with “From Recorders” sub-directories.

/Volumes
   Bio
      Bio 2020
         From Recorders
      Bio 2021
         From Recorders
      Bio 2022
         From Recorders
      Bio 2023
         From Recorders
      Bio 2024
         From Recorders
      Bio 2025
         From Recorders