This repository holds code accompanying the article "Individual identity information persists in learned calls of introduced parrot populations" in PLOS Computational Biology:
Smith-Vidaurre G, Pérez-Marrufo V, Hobson EA, Salinas-Melgoza A, Wright TF (2023) Individual identity information persists in learned calls of introduced parrot populations. PLoS Comput Biol 19(7): e1011231. https://doi.org/10.1371/journal.pcbi.1011231
The corresponding author of the associated paper (Grace Smith-Vidaurre) is also the code owner of this repository. The repository contains 10 R Markdown files in the main directory. The folder "functions" has 2 customized functions that are used in some analyses, and the folder "images" has several image files used for R Markdown knitting. The R Markdown files are numbered roughly in the order in which analyses were performed (Code_01 up to Code_10).
Each R Markdown file (extension .Rmd) has an associated HTML file (extension .html) with the knitted R Markdown output. This knitted output contains code annotations, code chunks, and the code output (summary statistics, statistics from different analyses, and visualizations). The knitted HTML files can be viewed by downloading each file and then opening each file with your default Internet browser (you can use the floating table of contents in each file to access different sections). The knitted output can be helpful for visualizing the expected results from different code chunks when using these R Markdown files to reproduce our analyses. Some analyses that rely on random sampling will not yield exactly the same results but should yield similar overall results. See the accompanying article for more information about accessing the data that can be used with this code to reproduce our analyses.
Please cite our article in PLOS Computational Biology, as well as this code if you find it useful for your own work 
This repository was archived on 12 June 2023, then unarchived/re-archived on 27 July 2023 after adding the citation for the associated article and data.