Dynamics of tree-cavity occupancy: Data and code

Supplementary Data and Code to the Manuscript Entitled “Dynamics of tree-cavity occupancy support the hypothesis that low use of avian-excavated cavities is driven by resource suitability”

The following list indicates the names of files included as supplementary data and code, as well as a brief description of their content. File names are given by headings in italic, followed by content description.

CavNestMisiones.rds 

Contains the data used to fit the model in file MSODynModel.R. It includes the following objects:

 y   An array with dimensions 452x20x16 showing the observed cavity states for each of 452 cavities, a maximum of 20 visits per cavity per year, and 16 years. This array contains NAs prior to the first year of cavity registration, after cavity loss, and in any year*visit combination for which there was no data for the corresponding cavity.

origen A vector with length 452 with ‘1’ for excavated and ‘2’ for non-excavated cavities.

MSODynModel.R

Model code including preliminary data processing, JAGS code for the dynamic multi-state occupancy model, and call to JAGS to fit the model. Model code includes posterior predictive checking for goodness-of-fit.

MSMO60k.Rdata

JAGs output with MCMC samples from the posterior probability distribution of model parameters.

SimCavs.R

Code for simulating cavity use.

SimCavsFunctions.R

Functions used in SimCavs.R.