Use SEEDLingS-Nouns in the scripts

Get the most recent public version

(Do this only once) Clone the seedlings-nouns repository to the "BLAB_DATA" folder in your home directory

Check if you've done this before with

git -C ~/BLAB_DATA/seedlings-nouns git status

One way to do this is to run the following in the terminal:

# It is ok if you already have the BLAB_DATA folder.
mkdir -p ~/BLAB_DATA &&
cd ~/BLAB_DATA &&
git clone https://github.com/BergelsonLab/seedlings-nouns.git

Run in the R console:

library(blabr)
get_latest_version('seedlings-nouns')

It will print the latest available public version. Let's say it was v1.0.0. Then use the following line in your code:

library(blabr)
seedlings_nouns <- get_seedlings_nouns('v1.0.0')

Repeat to update the version.

Get other files from the dataset

To get the information stored in regions.csv, recordings.csv, sub-recordings.csv (see Files or README.md in the repository), use

get_seedlings_nouns(version = 'v?.?.?', table = 'regions')

To get the codebooks, set the get_codebook parameter to TRUE. It can be combined with the table parameter.

Why are regions so weird?

Only the parts that were listened to are in the dataset. So, a (02:12:06-03:12:06) original annotated subregion that overlaps with a (02:52:06-03:32:06) silent region, will be represented as a (02:12:06-02:52:06) subregion in the dataset.

Get the most current development version

If recent changes to the annotations haven't made it to the public version of seedlings-nouns yet, and you really need those changes, you can use the development version. Here is how:

• Clone the seedlngs-nouns_private repository to ~/BLAB_DATA:

  mkdir -p ~/BLAB_DATA
  git clone https://github.com/BergelsonLab/seedlings-nouns_private.git

• Find the latest development version:

  blabr::get_latest_version('seedlings-nouns_private')

• Then use the printed-out version in the get_seedlings_nouns call.

• Set a reminder to switch to the public version before sending the script outside of BLab.

I use all_basiclevel, do I need to switch to SEEDLingS-Nouns?

If you don't know what all_basiclevel is - ignore this section.

all_basiclevel will keep being updated. So, if your script is using it and you don't want to switch to seedlings-nouns yet - that's fine. However, all_basiclevel doesn't have a public version, so you will still need to do the switch before sharing your code outside of BLab.