McCain CM, SRB King, TM Szewczyk. 2020. Unusually large upward shifts in cold-adapted, montane mammals as temperature warms. Ecology.
Code repository accompanying the manuscript.
- data/ contains data files, including raw files and files produced by scripts in this repository.
- Mamm_Summary_Data.csv: Elevational minimum, maximum, and number of detections for each species in each moutain range and era
- Mamm_FR_50m.csv: Detection data for the Front Range at 50m elevational bins
- Mamm_SJ_50m.csv: Detection data for the San Juans at 50m elevational bins
- prDet_processed.csv: Prior distributions for species' detection probabilities
- sample_els_C.csv: County, elevation, and species for contemporary detections
- sample_els_H.csv: County, elevation, and species for historic detections
- occupancy_mtn.csv: Summaries from repeatedly sampled sites for comparison with occupancy models
- CO_SiteInfo.txt: Basic information for repeatedly sampled 2010-2012 sites (Appendix S2)
- orig/: .xlsx files with a sheet for each species
- sites/: .txt files with data for repeatedly sampled sites
- code/ contains R scripts for processing data and running models
- 00_fn.R: Functions for simulations
- 1_dataProcessing.R: Code for munging raw data
- 2_mainModel.R: Code for running the undersampling model for each era x mtn
- 3_priorPredictions.R: Code for prior predictive checks
- 4_sensitivityAnalysis.R: Code for simulating communities & assessing impact of elevational bin size and sampling effort
- 5_occupancyComparison.R: Code for running the undersampling model and an occupancy model for comparison with only the repeatedly sampled sites
- models/: JAGS models
- out/ output produced by running the scripts in code/
- figs/ select figures produced by running the scripts in code/