Analysis of capture-recapture data for Sonoran desert tortoises from long-term monitoring plots across Arizona.
multistate-model.R: loads capture-recapture and covariate data, runs a Bayesian multi-state model using the nimble package, and summarizes model results.
- CapRecapData.csv: Capture-recapture data for all tortoises that were marked between 1987 and 2020 at each of 17 long-term monitoring plots.
- plot: 2-letter code for each of the 17 plots
- yr: capture year
- obsdate: capture date (YYYY-MM-DD format)
- tort: unique alphanumeric ID for each tortoise
- sex: Sex of tortoise, where 1 = female, 2 = male, and 3 = unknown (most of which are juveniles).
- MCL: Maximum carapace length
- Plots_NoCoords.csv: Covariate data for each plot.
- plot: 2-letter code for each of the 17 plots
- climate: climate division
- city.km: distance (km) from each plot to the center of the nearest city with ???10,000 people (based on 2010 US Census data).
- pptnorms.mm: Mean annual precipitation (mm) at each plot (data from PRISM)
- PDSI.csv: Monthly measures of Palmer drought severity index (PDSI) for climate divisions in Arizona from 1985 to 2020.
- div: climate division
- yr: year
- mon: month
- pdsi: PDSI value (data from the National Climatic Data Center)
- Precip_Monthly.csv: Monthly precipitation totals for each plot from 1985 to 2020.
- plot: 2-letter code for each of the 17 plots
- yr.m: year and month (YYYY-MM format)
- ppt: Cumulative precipitation (mm; data from PRISM)
- Surveys.csv: Summaries of survey effort at each plot from 1987 to 2020.
- plot: Name of plot
- code: 2-letter code for each of the 17 plots
- area.sqmi: area (sq. km) of each plot
- yr: Survey year
- persondays: number of person days spent searching a plot for tortoises in a given year.