Code to Examine How the Influence of Fine-Scale Habitat Characteristics on Greater Sage-Grouse (Centrocercus urophasianus) Nest Site Selection and Nest Survival Varies by Mesic and Xeric Site Conditions version 1.0

This repository centralizes R code used to examine how the influence of fine-scale habitat characteristics on Greater sage-grouse (Centrocercus urophasianus) nest site selection and nest survival varies by mesic and xeric site conditions, utilizing data collected from a wide range of study sites in Nevada and California, USA.

The R script "nest_selection_model.R" provides code for a GLMM framework within a Bayesian modeling environment to evaluate the effects of fine-scale habitat predictors on nest site selection. The R script "nest_survival_model.R" provides code for a Bayesian shared frailty model framework that estimates impacts of fine-scale habitat covariates on daily hazard rates and nest-survival of sage-grouse. For both models, to allow for site-level variation in effects of habitat predictors among sites, the script implements a random slopes model, estimating an intercept and slope for each site (Gillies et al. 2006, Gelman and Hill 2007, Kery 2010). Site-level intercepts and coefficients are drawn from a multivariate normal distribution, with a grand mean intercept and slope coefficient estimated for each hydrographic region (i.e. mesic versus xeric sites). Variance and covariance parameters representing site intercept, slope, and slope-intercept covariance, respectively, are also estimated based on the hydrographic region assignment for each site (Kery 2010). To facilitate estimation of the variance-covariance matrix, we specified the scaled-inverse Wishart prior distribution (Gelman and Hill 2007). All models (nest selection and survival) are carried out using JAGS 4.2.0 (R version 3.4.3) and the package jagsUI (Kellner 2015).
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This code release accompanies the following manuscript:
Brussee, B.E., Coates, P.S., O'Neil, S.T., Ricca, M.A., Dudko, J.E., Espinosa, S.P., Gardner, S.C., Casazza, M.L., and Delehanty, D.J., 2023, Influence of fine-scale habitat characteristics on sage-grouse nest site selection and nest survival varies by mesic and xeric site conditions. Ornithological Applications, duac052, https://doi.org/10.1093/ornithapp/duac052.

To cite the code, please use:
Brussee, B.E., and Coates, P.S. Code to examine how the influence of fine-scale habitat characteristics on Greater Sage-grouse (Centrocercus urophasianus) nest site selection and nest survival varies by mesic and xeric site conditions version 1.0: U.S. Geological Survey software release, https://doi.org/10.5066/P9EWKWJ3.

To cite the data, please use:
Brussee, B.E., Coates, P.S., O'Neil, S.T., Ricca, M.A., Dudko, J.E., Espinosa, S.P., Gardner, S.C., Casazza, M.L., Delehanty, D.J. and Chenaille, M.P., 2022, Microhabitat characteristics influencing sage-grouse nest site selection and survival, Nevada and California (2012 - 2017): U.S. Geological Survey data release, https://doi.org/10.5066/P9JJ747B.

References:
Gelman, A., and Hill, J. (2007). Data analysis using regression and multilevel/hierarchical models: New York, New York, Cambridge University Press.

Gillies, C.S., Hebblewhite, M., Nielsen, S.E., Krawchuk, M.A., Aldridge, C. L., Frair, J.L., Saher, D.J., Stevens, C.E., and Jerde, C.L. (2006). Application of random effects to the study of resource selection by animals. Journal of Animal Ecology 75, 887-898.

Kellner, K. (2015). jagsUI: a wrapper around rjags to streamline JAGS analyses.

Kery, M. (2010). Introduction to WinBUGS for ecologists: Bayesian approach to regression, ANOVA, mixed models and related analyses: Cambridge, Massachusetts, Academic Press.