Code associated to 'Large-scale informative priors to better predict the local occurrence rate of a rare tree-related microhabitat'

This archive presents codes and functions in R programming language that were used in "Using informative priors to better quantify the occurrence rate of a rare tree-related microhabitat locally" by P. Cottais et al. (doi : 10.1101/2024.11.28.625900). The archive is made of seven files :

• RepriseFL_vPub_R1.rmd is a RMarkdown file that presents the global pipeline of analyses used in the study of P. Cottais et al.;
• RepriseFL_vPub_R1.pdf is a compiled version of Main.rmd in a more readable pdf format;
• ggplots.R is a R source file containing functions to generate some graphical outputs, it is called by Main.rmd;
• chains_process.R is a R source file containing custom-made functions to handle MCMC outputs , it is called by Main.rmd;
• Weibull_Hierarchic_11A_Rot.Hole_Chains.txt is a text file containing the MCMC output of Courbaud et al (2022) continental model, used in building informative priors in the study of P. Cottais et al. , , it is read by Main.rmd;
• model_nonInfo_vPub_R1.r is a R source file creating functions to run bayesian estimation with non informative priors; 
• model_Info_vPub_R1.r is a R source file creating functions to run bayesian estimation with informative priors.

The tree census data used in the code has been provided as a separate repository : 10.5281/zenodo.14231133