snowy_plover_eggs

Reproducible datasets and code for:

Egg size variation in the context of polyandry: a case study using long-term field data from snowy plovers

Luke J. Eberhart-Hertel, Lourenço Falcão Rodrigues, Johannes Krietsch, Anne G. Eberhart-Hertel, Medardo Cruz López, Karina Alejandra Vázquez-Rojas, Erick González-Medina, Julia Schroeder, and Clemens Küpper

Evolution, qpad168, https://doi.org/10.1093/evolut/qpad168

In this repository you can find all the raw data and code needed to reproduce our investigation of egg size variation in snowy plovers (Charadrius nivosus) monitored annually since 2006 at Bahía de Ceuta – an important breeding site in western Mexico.

For a complete overview of the methods and results presented in our manuscript, please view our project vignette: Supplementary File 1

Egg size variation and its relationship to chick size in snowy plovers (Charadrius nivosus). Illustrations and photo by Luke Eberhart-Hertel.

Repository Contents

R/

• project_X.R scripts contain housekeeping code (custom functions, loading libraries, plotting themes, etc.)
• wrangle_X.R scripts contain code used to wrangle the CeutaOPEN database into the format used in the models presented in this investigation
• model_X.R scripts contain code used for modeling and exporting output
• results_X.R scripts contain code used to process the model output into figures and tables

data/

• mol_sex.rds is the molecular sex-type data for a subsample of the individuals in the ceuta_egg_chick_female_data.rds
• chicks_2006_2020.rds
• BaSTA_checked_life_table_females_2006-2020.rds is the processed BaSTA file containing the encounter histories of all individually marked plovers in the population
• ceuta_egg_chick_female_data.rds is the trait data used in the polyandry, egg volume, and lay date models
• raw_encounter_histories_females_2006_2020.rds is the raw unprocessed encounter histories of all individually marked plovers in the population with each row being an encounter.
• raw_life_table_females_2006_2020.rds is the raw unprocessed encounter histories of all individually marked plovers in the population with each row being an individual and columns including annual detections (i.e., the main difference with the BaSTA life table file is that this contains the individual identities)

output/

• multibasta_output_females_min_age_1_2006-2020.rds is the output from the BaSTA modl selection
• stats_eggv_mod.rds is the output from the egg volume model
• stats_polyandry_age_mod.rds is the output from the polyandry model
• stats_renesting_mod.rdsis the output from the re-nesting model
• stats_laydate_mod.rds is the output from the lay date model
• stats_chick_mod.rds is the output from the chick weight model
• age_estimate_uncertainty_bootstraps.rds is the output form the BaSTA age uncertainty bootstrap

products/figures/

• Figure_1.jpg: BaSTA survival function
• Figure_2.jpg: sampling distribution
• Figure_3.jpg: egg volume and lay date models forest plots
• Figure_4.png: seasonal correlates
• Figure_5.jpg: lay date variation by age and origin
• Figure_S1.jpg: raw egg size variation
• Figure_S2.png: BaSTA model diagnostics
• Figure_S3.jpg: chick model forest plot
• Figure_S4.jpg: polyandry model forest plot
• Figure_S5.jpg: re-nesting model forest plot
• Figure_S6.jpg: residuals plot
• Figure_S7.jpg: tarsus correlates
• Figure_S8.jpg: BaSTA age uncertainty plots

products/tables/

• Table_S1.png: BaSTA model selection results
• Table_S2.png: chick weight model results
• Table_S3.png: egg volume model results
• Table_S4.png: polyandry model results
• Table_S5.png: re-nesting model results
• Table_S6.png: lay date model results