What is bat2inat

bat2inat is a collection of R functions that make it possible for those familiar with R to bulk upload bat call files from wildlife acoustics recorders to iNaturalist. It is important that when uploading bat calls to iNaturalist that as much information as possible is shared to support the verification of the records. bat2inat ensures that this is done by uploading date, time, location, call parameters, spectrograms and the sound file to iNaturalist.

Please manually check the identification of all calls before uploading to iNaturalist

Getting set up

There are a few things you will need to sort out before we can start uploading files.

0. Clone this repository into your RStudio. Go File > New Project > Version Control > Git > Under repository URL put 'https://github.com/AugustT/bat2inat'

1. Create an app on iNat here: https://www.inaturalist.org/oauth/applications/new, make not of the application ID and application secret.

2. Save out your id, secret, username and password to an object and don't share it with others. Add it to your .gitignore if you are using git.

You can do this last stage like this:

token <- list(username = "<YOUR_USENAME>",
              password = "<YOUR_PASSWORD>",
              app_id = "<APPLICATION_ID>",
              app_secret = "<APPLICATION_SECRET>")

save(token, file = 'token.rdata')

3. Install the R packages we will need

list.of.packages <- c('av', 'reticulate',
                     'bioacoustics', 'webshot')
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

4. Install the pynaturalist package

If you do not have python installed on your system you will be prompted to install miniconda, this is required for the uploader to work so please say 'yes'.

library(reticulate)

py_install("pyinaturalist==0.14.0dev374", pip = TRUE)

6. Test out a simple upload. If this works you should see a new observation appear in your iNaturalist account

load('token.rdata')

# Start using the package
pynat <- import('pyinaturalist')

# get token
token <- pynat$get_access_token(token[[1]],
                                token[[2]],
                                token[[3]],
                                token[[4]])

# Submit an observation
pynat$create_observation(
  species_guess = 'Chiroptera',
  observed_on = '2021-05-02 11:23',
  description='This is a test upload, not a real observation',
  latitude = 51.5998, 
  longitude = -1.1308,
  positional_accuracy = 10,
  access_token = token
)

6. Upload and bat call file

This will upload one of the call files shipped with the code. If it works you will see a new record in your iNaturalist account, dont forget to delete it.

# Load in the R functions
for(file in list.files('functions', full.names = T)) source(file)
library(reticulate)

# Import the uploader
pynat <- import('pyinaturalist')

# Choose the file to upload
file <- 'data/BARBAR_20210526_221302.wav'

# load your token
load('token.rdata')

# Upload the observation
send_observation(file = file, 
                 post = TRUE, 
                 token = token)

7. Batch upload call files

You can point R to a director and get it to list all the wav files in that folder, and all sub folders. This is a quick way to use this to upload all your call files in a folder. If it works you will see a batch of new records in your iNaturalist account, dont forget to delete them.

# Load in the R functions
for(file in list.files('functions', full.names = T)) source(file)
library(reticulate)

# Import the uploader
pynat <- import('pyinaturalist')

# Choose the files to upload
files <- list.files(path = 'data',
                    pattern = '.wav',
                    recursive = T,
                    full.names = T)
                    
# load your token
load('token.rdata')

# Upload the observations
ids <- lapply(X = files,
              FUN = send_observation,
              token = token)