Data/Code for Guzy et al_2019_Influence of riparian buffers and habitat characteristics on salamander assemblages in headwater streams within managed forests

This repository includes data, code for the model, and code to make basic plots for the hierarchical salamander community occupancy model of [Guzy, J., Halloran, K., Homyack, J. and Willson, J.D., 2019. Influence of riparian buffers and habitat characteristics on salamander assemblages in headwater streams within managed forests. <i>Forest Ecology and Management</i>, <i>432</i>, pp.868-883. https://doi.org/10.1016/j.foreco.2018.10.006 ]We sampled salamanders with repeated, time, and area-constrained surveys within riparian streamside management zones (SMZs) during April–June 2014, 2015, and 2016. We used a multi-species, hierarchical Bayesian model developed by Zipkin et al. (2009) and modified by Hunt et al. (2013) to estimate species-specific occupancy responses to site-specific covariates (average SMZ width, stand age categories, SMZ composition, Site PC1, and Site PC2) and sampling covariates (PC1 and PC2). Data include Species occurrence files (n=10 species) are stored as a .csv for each species which includes presence-absence data for 102 sites during 4 surveys. Data are brought into Program R, and the model is run using the package R2Winbugs. The provided code ("Multi_species_occupancy_annotated_Guzy_et_al_2019.R") reads in each species and compiles one large encounter matrix ('X') which gets sent to the model. Site covariates are provided in file titled "Site Covariates". Sampling covariates are provided in the files titled "pc1" and "pc2". The annotated model is provided as well as code to generate some basic plots.