Data and R code from: Spatiotemporal risk factors predict landscape-scale survivorship for a northern ungulate
Cite this dataset
Eacker, Daniel; Jakes, Andrew; Jones, Paul (2022). Data and R code from: Spatiotemporal risk factors predict landscape-scale survivorship for a northern ungulate [Dataset]. Dryad. https://doi.org/10.5061/dryad.pvmcvdnnt
These data and computer code (written in R, https://www.r-project.org) were created to statistically evaluate a suite of spatiotemporal covariates that could potentially explain pronghorn (Antilocapra americana) mortality risk in the Northern Sagebrush Steppe (NSS) ecosystem (50.0757o N, −108.7526o W). Known-fate data were collected from 170 adult female pronghorn monitored with GPS collars from 2003-2011, which were used to construct a time-to-event (TTE) dataset with a daily timescale and an annual recurrent origin of 11 November. Seasonal risk periods (winter, spring, summer, autumn) were defined by median migration dates of collared pronghorn. We linked this TTE dataset with spatiotemporal covariates that were extracted and collated from pronghorn seasonal activity areas (estimated using 95% minimum convex polygons) to form a final dataset. Specifically, average fence and road densities (km/km2), average snow water equivalent (SWE; kg/m2), and maximum decadal normalized difference vegetation index (NDVI) were considered as predictors. We tested for these main effects of spatiotemporal risk covariates as well as the hypotheses that pronghorn mortality risk from roads or fences could be intensified during severe winter weather (i.e., interactions: SWE*road density and SWE*fence density). We also compare an analogous frequentist implementation to estimate model-averaged risk coefficients. Ultimately, the study aimed to develop the first broad-scale, spatially explicit map of predicted annual pronghorn survivorship based on anthropogenic features and environmental gradients to identify areas for conservation and habitat restoration efforts.
We combined relocations from GPS-collared adult female pronghorn (n = 170) with raster data that described potentially important spatiotemporal risk covariates. We first collated relocation and time-to-event data to remove individual pronghorn from the analysis that had no spatial data available. We then constructed seasonal risk periods based on the median migration dates determined from a previous analysis; thus, we defined 4 seasonal periods as winter (11 November–21 March), spring (22 March–10 April), summer (11 April–30 October), and autumn (31 October–10 November). We used the package 'amt' in Program R to rarify relocation data to a common 4-hr interval using a 30-min tolerance. We used the package 'adehabitatHR' in Program R to estimate seasonal activity areas using 95% minimum convex polygon. We constructed annual- and seasonal-specific risk covariates by averaging values within individual activity areas. We specifically extracted values for linear features (road and fence densities), a proxy for snow depth (SWE), and a measure of forage productivity (NDVI). We resampled all raster data to a common resolution of 1 km2. Given that fence density models characterized regional-scale variation in fence density (i.e., 1.5 km2), this resolution seemed appropriate for our risk analysis.
We fit Bayesian proportional hazards (PH) models using a time-to-event approach to model the effects of spatiotemporal covariates on pronghorn mortality risk. We aimed to develop a model to understand the relative effects of risk covariates for pronghorn in the NSS. The effect of fence or road densities may depend on SWE such that the variables interact in affecting mortality risk. Thus, our full candidate model included four main effects and two interaction terms. We used reversible-jump Markov Chain Monte Carlo (RJMCMC) to determine relative support for a nested set of Bayesian PH models. This allowed us to conduct Bayesian model selection and averaging in one step by using two custom samplers provided for the R package 'nimble'.
For brevity, we provide the final time-to-event dataset and analysis code rather than include all of the code, GIS, etc. used to estimate seasonal activity areas and extract and collate spatial risk covariates for each individual. Rather we provide the data and all code to reproduce the risk regression results presented in the manuscript.
Please refer to ReadMe file.
National Fish and Wildlife Foundation, Award: 70724