Red-headed Woodpecker Parental Care

This repository contains data, code, analyses, and plots by L. Abigail Walter for research on Red-headed Woodpecker (RHWO) parental care behavior with the Bulluck Avian Ecology Lab at Virginia Commonwealth University. The data in this repository are covered by the CC BY-NC-SA license.

Publication

You can read the paper online or download a pdf. 📄

Field methods

Please refer to our manuscript for a detailed summary of data collection.

Metadata

• Field definitions for raw data: raw_data/readme.md
• Field definitions for clean data: clean_data/readme.md

Requirements

• R Version: v3.5.2+
• Packages: tidyverse, lubridate, reshape2, glmmTMB, AICtab, psych, cowplot

Data wrangling

Please note that it is not strictly necessary to run the following R scripts. Clean data files are already included in /clean_data. Their creation is nevertheless outlined below.

Incubation

• Run scripts/incubation/wrangling_incubation.R to wrangle and tidy the raw data into clean_data/incubation.rds.

Brooding, provisioning, and nest cleaning

• Run scripts/wrangling_parentalcare.R to wrangle and tidy the raw data into clean_data/behaviors.csv.

Data analyses

The following scripts are used to analyze incubation, brooding, provisioning, and nest cleaning behaviors using the clean data files (generated above). Also described are files used to check effects of GPS tags on RHWO behavior, summarize nest success, and calculate nest check frequency.

Incubation

• To analyze the incubation data, run scripts/incubation/incubation_analysis.R
• To plot, run scripts/cleaning/incubation_and_cleaning_plot.R

Brooding

1. Run scripts/brooding/brooding_models.R to follow the modeling process and see how the "top GLMM" was chosen.
2. Plot predictions using scripts/brooding/brooding_plots.R
3. View boxplots of brooding by sex with and without behavior classified as "poopsearch" (in cavity for any amount of time, emerge with fecal sac) with scripts/brooding/poopsearch_justification.R. Excluding those visits did not change male brooding mean duration.
4. Generate additional summary statistics pertaining to brooding durations using scripts/brooding/brooding_duration.R

Provisioning

1. Run scripts/provisioning/provisioning_models.R to follow the modeling process and see how the "top GLMM" was chosen.
2. Plot predictions using scripts/provisioning/provisioning_plots.R
3. Plot individual variation in provisioning using scripts/provisioning/provisioning_individuals.R
4. Run additional analyses on reasons for variation in female provisioning using scripts/provisioning/provisioning_individuals_extra.R

Nest cleaning

• Run scripts/cleaning/cleaning_analysis.R for analysis.
• To plot, run scripts/cleaning/incubation_and_cleaning_plot.R

GPS tags

Since some woodpeckers were GPS tagged for another part of our study, we checked to see if they caused a difference in parental care rates.

1. Run scripts/gps-tags/gps_tag_parentalcare.R to analyze effects of GPS tags on behavior.
2. Run scripts/gps-tags/gps_tag_provisioning_individuals.R to analyze effects of GPS tags on individual provisioning.

Nest success

• Summaries of fledge success can be found in scripts/summary_stats.R
• Nest check analyses are in scripts/nest_monitoring/nest_check_frequency.R

Other files

Deprecated R scripts are moved to the /archive directory.

Acknowledgments

We used program BORIS to process videos and generate raw csv files.