Data, R code, and Stan code for "Ecological harshness has a weak influence on reproductive trade-offs in a great tit population"

Ecological harshness has a weak influence on reproductive trade-offs in a great tit population This repository hosts data, R code, and Stan code for Bliard L, Martin JS, Childs DZ, Cole EF, Sheldon BC, Paniw M, Ozgul A. Ecological harshness has a weak influence on reproductive trade-offs in a great tit population. Published article: https://doi.org/10.1093/jeb/voag011 Preprint version: https://doi.org/10.32942/X26629 GENERAL INFORMATION 1. Title: Data and scripts from "Ecological harshness has a weak influence on reproductive trade-offs in a great tit population". 2. Author Information: A. Name: Louis Bliard Institution: University of Zurich (now Aarhus University) Email: bliard.louis@gmail.com B. Name: Jordan S Martin Institution: Eawag - Swiss Federal Institute of Aquatic Science and Technology C. Name: Dylan Z Childs Institution: University of Sheffield D. Name: Ella F Cole Institution: University of Oxford E. Name: Ben C Sheldon Institution: University of Oxford F. Name: Maria Paniw Institution: Estación Biológica de Doñana G. Name: Arpat Ozgul Institution: University of Zurich 4. Date of data collection: 1961-2018 5. Geographic location of data collection: 51°77′N, 1°32′W SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC-BY 4.0 2. Links to publications that cite or use the data: https://doi.org/10.32942/X26629 3. Links to other publicly accessible locations of the data: SPI-Birds https://nioo.knaw.nl/en/projects/spi-birds/study/wytham-woods 4. Was data derived from another source? NA 5. Recommended citation for this dataset: Bliard L, Martin JS, Childs DZ, Cole EF, Sheldon BC, Paniw M, Ozgul A (2026). Ecological harshness has a weak influence on reproductive trade-offs in a great tit population [Data set]. DATA & FILE OVERVIEW 1. File List: a. Data - data_wytham_tits.RData - df.txt - df_fecundity.txt b. Model - model_wytham_tits.stan - model_no_season_re.stan c. Analyses - analysis_wytham_tits.R - analysis_no_imputation.R - analysis_interaction_beechmast_density.R d. Output - posterior_draws.txt - posterior_draws_interaction.txt - posterior_draws_no_imputation.txt - posterior_draws_no_season_re.txt - posterior_draws_no_season_re_no_env.txt e. Figure - figures_effects_on mean_traits.R - figures_effects_on_correlations.R - figures_effects_on_trait_variance.R - figure_brood_reduction.R - comparison_prior_hyperbolic_tangent.R - figure_interaction_beech_mast_density.R 2. Relationship between files, if important: The RData file data_wytham_tits.RData contains the datasets df.txt and df_fecundity.txt, as well as 20 alternative versions of these datasets with imputed missing data mi.df and mi.df.fecundity. These datasets are needed to run all the analyses. The Stan code file model_wytham_tits.stan is the main statistical model, which can be run using the main analysis R script analysis_wytham_tits.R. The output (i.e. posterior samples, that comprise 60000 posterior samples per parameter) of this model is stored in the file posterior_draws.txt. The same statistical model can be performed excluding the imputed data using the R script analysis_no_imputation.R. The output of this model is stored in the file posterior_draws_no_imputation.txt. The same statistical model can be performed including an interaction between beech mast index and population density using the R script analysis_interaction_beechmast_density.R. The output of this model is stored in the file posterior_draws_interaction.txt. To perform the statistical model that does not include the year random effect, the Stan code file model_no_season_re.stan needs to be used. The output of this model is stored in the file posterior_draws_no_season_re.txt. The posterior_draws.txt file can be used together with the R script figures_effects_on_correlations.R to reproduce Figure 1, Figure 2, Figure 3, and Figure 4 of the manuscript. The R script figure_brood_reduction.R can be used to reproduce Figure S1. The posterior_draws_no_imputation.txt file can be used together with the R script figures_effects_on_correlations.R and figures_effects_on mean_traits.R to reproduce Figure S3 and Figure S4 of the manuscript. The R script comparison_prior_hyperbolic_tangent.R can be used to reproduce Figure S5 of the manuscript. The posterior_draws_no_season_re.txt file can be used together with the R script figures_effects_on_correlations.R to reproduce Figure S6 of the manuscript. The posterior_draws_no_season_re_no_env.txt file can be used together with the R script figures_effects_on_correlations.R to reproduce Figure S7 of the manuscript. The posterior_draws_interaction.txt file can be used together with the R script figure_interaction_beech_mast_density.R to reproduce Figure S8 and Figure S9 of the manuscript. The posterior_draws.txt file can be used together with the R script figures_effects_on mean_traits.R to reproduce Figure S10 and Figure S11 of the manuscript. The posterior_draws.txt file can be used together with the R script figures_effects_on_trait_variance.R to reproduce Figure S12, Figure S13, Figure S14, and Figure S15 of the manuscript. METHODOLOGICAL INFORMATION 1. Methods for processing the data: R. Only the formatted data for analysis is provided. Please contact the data custodian in charge of the great tit data (Ben Sheldon) if you wish to access the great tit and blue tit database for your own analyses. 2. Instrument- or software-specific information needed to interpret the data: - R v.4.3.2 https://www.r-project.org/ - CmdStanR v.0.8.1 https://mc-stan.org/cmdstanr/ 3. People involved with sample collection: Ella F Cole, Ben C Sheldon 4. People involved with data formatting and analysis: Louis Bliard 5. for more general information regarding the methods, see https://doi.org/10.1111/2041-210X.70125 and the related code https://github.com/Jordan-Scott-Martin/covariance-reaction-norms and https://doi.org/10.1111/1365-2656.14173 and the related code https://github.com/lbiard/detecting_tradeoffs_crn_models DATA-SPECIFIC INFORMATION FOR: data_wytham_tits.RData 1. Number of objects: 4 2. Objects List: - "df.txt" = data frame containing data for the offspring mass model. - "df_fecundity.txt" = data frame containing data for the fecundity and recruitment models. - "mi_df" = list of 20 data frames, with same format as "df.txt" but with imputed missing data. - "mi_df_fecundity" = list of 20 data frames, with same format as "df_fecndity.txt" but with imputed missing data. DATA-SPECIFIC INFORMATION FOR: df.txt 1. Number of variables: 19 2. Number of cases/rows: 53753 Each row correspond to one offspring. 3. Variable List: - "BreedingSeason" = year of the observation. - "FemaleID" = unique identifier of the mother. - "BroodIDLaid" = unique identifier of the brood. - "IndivID" = unique identifier of the offpsring. - "CapturePlot" = location within Wytham woods. - "Mass.x" = mass of the offpsring (in grams). - "ChickAge" = age of the offspring at the time of mass measurement. - "Plot" = location within Wytham woods. - "LocationID" = unique identifier of the nextbox. - "LayDate_observed" = lay date of the brood in Julian days starting on April 1st. - "BroodSize_observed" = size of the brood. - "Mass.y" = mass of the mother (in grams). - "breeding_age" = age of the mother (0 = 1st year bird; 1 = 2+ year bird). - "spring_temperature" = daily mean temperature from March 1st to May 9th (in Celsius). - "spring_precipitation" = sum of precipitation from April 1st to May 31st (in mm). - "population_density" = number of females hatching at least one egg in the given breeding season. - "Half_fall_date" = day of peak abundance of winter moth larvae. - "mast.score" = beech mast index, scored as an ordinal variable of increasing beech mast from 0 to 2 - "synchrony" = difference (in days) between the half fall date and the mother's laying date. 4. Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: df_fecundity.txt 1. Number of variables: 16 2. Number of cases/rows: 7287 Each row correspond to one brood. 3. Variable List: - "BroodID" = unique identifier of the brood. - "BreedingSeason" = year of the observation. - "FemaleID" = unique identifier of the mother. - "Plot" = location within Wytham woods. - "LocationID" = unique identifier of the nextbox. - "LayDate_observed" = lay date of the brood in Julian days starting on April 1st. - "BroodSize_observed" = size of the brood. - "Mass" = mass of the mother (in grams). - "breeding_age" = age of the mother (0 = 1st year bird; 1 = 2+ year bird). - "spring_temperature" = daily mean temperature from March 1st to May 9th (in Celsius). - "spring_precipitation" = sum of precipitation from April 1st to May 31st (in mm). - "population_density" = number of females hatching at least one egg in the given breeding season. - "n_recruits" = number of offpsring from the brood that have recruited into the population in following years. - "Half_fall_date" = day of peak abundance of winter moth larvae. - "mast.score" = beech mast index, scored as an ordinal variable of increasing beech mast from 0 to 2 - "synchrony" = difference (in days) between the half fall date and the mother's laying date. 4. Missing data codes: NA