Drivers of diurnal variation in vocal activity in a tropical bird community

This repository contains code and analysis for a manuscript that examines the drivers of diurnal variation in vocal activity for a tropical bird community in the Western Ghats.

This manuscript is currently in review. Please reach out to the repository owner if you have questions.

Readable version

A readable version of this analysis is available in bookdown format by clicking on the heading above.

Source code for the analyses

We describe what each script (.Rmd) of this repository is intended to achieve below.

• 01_data-cleaning.Rmd:. This script is intended to clean data and ensure that the appropriate columns are available for further analyses and calculations. specifically, we combine data from dawn and dusk into a single object/.csv for independent use. To access the output from this script, head over to results/acoustic-data.csv.

• 02_vocal-activity.Rmd:. Here, we calculate differences in vocal activity between dawn and dusk for the entire community and for each species, separately.

• 03_frequency.Rmd: Here, we test the predictions of the acoustic transmission hypothesis by testing associations between the median peak frequency (at which a species vocalizes) and the number of acoustic detections at dawn and dusk.

• 04_light-availability.Rmd: Here, we test the predictions of the Inefficient foraging hypothesis by examining how vocal activity varies as a function of time_to_darkness - a proxy measure for total daytime light levels.

• 05_foraging-guild.Rmd: Here we examine if vocal activity significantly differs across foraging guild categories (frugivore/omnivore/invertivore).

• 06_territoriality.Rmd: Here, we examine if vocal activity significantly differs across categories of territoriality (highly territorial/weakly territorial/non-territorial).

• 07_sociality.Rmd: Here, we examine if vocal activity significantly differes across levels of communal signaling (communal/non-communal signalers).

• 08_pgls-analysis.Rmd: Here, we test which environmental or social factor/combination of factors best explains dawn-biased vocal activity.

Data

The data/ folder contains the following datasets required to reproduce the above scripts.

• birdtree.nex: This file contains the list of phylogenetic trees required for the PGLS analysis (accessed from https://birdtree.org).

• frequency-data.csv: This file contains high-quality vocalizations for 114 species of birds and associated measurements.

• list-of-sites.csv: Contains the list of sites across which audio recorders were deployed along with ancillary information, including latitude, longitude.

• sociality-data.csv: Contains information on whether a species is a communal signaller or a non-communal signaller (accessed from Tobias et al. 2016).

• species-annotation-codes.csv: Contains list of species common, scientific names and eBird species codes for standardization.

• species-trait-dat.csv: Contains information on foraging guild type for each species, accessed from the State of India's Birds Report (2023) and AVONET trait database (Tobias et al. 2022).

• territoriality-data.csv: Contains information on whether a species is highly territorial, weakly territorial or non-territorial (accessed from Tobias et al. 2016).

Results

This folder contains outputs that were obtained by running the above scripts.

• acoustic-data.csv: This file contains the output from 01_data-cleaning.Rmd and includes the data required to run all the analysis associated with this study.

• metadata-detections-lightAvailability-correlations.csv: This file contains the metadata from running a Pearson's correlation test between the number of acoustic detections and time to darkness for all species for dawn and dusk, separately.

Figures

The figs\ folder contains figures accompanying the main text, as well as supplementary material figures.

Attribution

To cite this repository:

Ramesh, Vijay and Sundar, Pavithra. (2023). Source code and supplementary material for (version xx). Zenodo. [doi to be added].