songdkl

About

automated quantitation of vocal learning in the songbird

As described in:
Mets, David G., and Michael S. Brainard.
"An automated approach to the quantitation of vocalizations and vocal learning in the songbird."
PLoS computational biology 14.8 (2018): e1006437.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006437&rev=2

Data for demo and testing is from the following Dryad data package:
Mets, David G.; Brainard, Michael S. (2019), Data from: An automated approach to the quantitation of vocalizations and vocal learning in the songbird., Dryad, Dataset, https://doi.org/10.5061/dryad.8tn4660
Dataset can be downloaded here:
https://datadryad.org/stash/dataset/doi:10.5061/dryad.8tn4660

Installation

as a user

$ pip install songdkl
We recommend installing into a virtual environment, in order to capture the compute environment for computational projects. For more information and good practices, please see:
https://the-turing-way.netlify.app/reproducible-research/renv.html

as a developer

This project uses the library nox as a task runner, to automate tasks like setting up a development environment. Each task is represented as what nox calls a "session", and you can run a session by invoking nox at the command-line with the name of the session.

So, to set up a virtual environment for development with songdkl installed in "editable" mode, run the "dev" session.

We suggest using pipx to install nox in an isolated environment, so that nox can be accessed system-wide without affecting anything else on your machine.

1. Install pipx, e.g. with brew (and brew works on Linux too)
2. Install nox with pipx: pipx install nox
3. Use nox to run the dev session: nox -s dev
4. Activate the virtual environment: . ./.venv/bin/activate (and/or tell your IDE to use it)

Usage

songdkl provides a command-line interface (cli) that allows the user to run the program from the terminal.

The cli makes two commands available:

• calculate, to compute the songdkl between two directories of songs, e.g., from 2 birds
  $ songdkl calculate bird1_dir bird2_dir

• numsyls, to estimate the number of syllables in a bird's song
  $ songdkl numsyls bird1_dir

For details on usage, please run songdkl --help.

Citation

If you use this software, please cite the DOI:

Please also cite the original paper: Mets, David G., and Michael S. Brainard.
"An automated approach to the quantitation of vocalizations and vocal learning in the songbird."
PLoS computational biology 14.8 (2018): e1006437.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006437&rev=2

@article{mets2018automated,
  title={An automated approach to the quantitation of vocalizations and vocal learning in the songbird},
  author={Mets, David G and Brainard, Michael S},
  journal={PLoS computational biology},
  volume={14},
  number={8},
  pages={e1006437},
  year={2018},
  publisher={Public Library of Science San Francisco, CA USA}
}

If you use the accompanying Dryad dataset, please cite that as well:
Mets, David G.; Brainard, Michael S. (2019), Data from: An automated approach to the quantitation of vocalizations and vocal learning in the songbird., Dryad, Dataset, https://doi.org/10.5061/dryad.8tn4660