/CES-Hungary

Adult sex ratios and true survival of male and female birds. Analyses of constant effort sites (CES) from Hungary.

Primary LanguageR

Analyses of constant effort sites (CES) from Hungary

We used data from 24'830 captures of 11 bird species, collected at 40 Hungarian constant effort ringing sites (CES), to estimate capture probability, site fidelity (the complement of dispersal), and true survival. A poster summary of the project can be found here.

General R-Files to process data and results

The following files are available in the R folder:

  • Data_processing.R: This script is loading the original data, is doing some data tests and saves the prepared data in RData/dat.RData. To run this script one needs access to the excel File with the original data (CES 2004_2015.xlsx).

  • Compile_Results.R: Loads the mcmc results for all species from the Ressim folder and calculates some summary statistics that were partly used in the manuscript.

  • Figures.R: Loads the mcmc results for all species from the Ressim folder and produces the figures presented in the manuscript. The resulting PDFs of the figures are saved in the Results folder.

Files to run Bugs model for each species

The files needed to run the model in JAGS (from R using rjags) are available in the JAGS folder:

  • CES.R: For one species this prepares the data for jags, all the settings for jags (including initial values, burn-in etc.), starts JAGS. As soon the run in JAGS is terminated the file also saves the mcmc results in the Ressim folder.

  • Model.R: Contains the formulation of the multi-state capture-recapture model (including priors) in BUGS-language.

  • Make_Files.R and job.sh are needed to run the analyses for all 11 species at the clusters of sciCORE of the University of Basel.