birdnet2sqlite: convert birdnet results to .sqlite database

How to use it

Install the poetry environment

poetry install

Run birdnet2sqlite.sh

A wrapper can be found in example_script.sh. You just need to change the arguments in the script and run it using:

./run.sh

With:

• BASE_FOLDER: The folder containing all the birdnet output files.
• DB_NAME: The name you want to give to the database. Note that it has to end with .sqlite (e.g. my_database.sqplite).
• IS_PREFIX: Is the filename formatted such as PREFIX_YYYmmdd_HHMMSS? Either True or False.
• INDEX_LOCATION_FOLDER: The position of the folder name that will be used as a location column in the database (e.g. INDEX_LOCATION_FOLDER would be set to -2 for path/to/data/LOCATION/file.txt).

Use the database in R

To open the created databse in R you can use the script below:

library(RSQLite)
library(DBI)

setwd("path/to/working/directory")
sqlite <- dbDriver("SQLite")
conn <- dbConnect(sqlite, "my_database.sqlite")

# For the full dataset
data <- dbReadTable(conn, "birdnet")

# For a subset of the dataset
res <- dbSendQuery(con, "SELECT * FROM birdnet WHERE location = X")