A workshop on mark-recapture analyses in R. This workshop uses the 'marked' package to construct open-population mark-recapture models in R. All examples use the 'dipper' dataset contained within the 'marked' package.
This workshop covers:
- Formatting data into capture histories
- Fitting Cormack-Jolly-Seber models to estimate survival and detection probability
- Testing the goodness-of-fit of Cormack-Jolly-Seber models
- Fitting Jolly-Seber models to estimate population size
- Fitting known-fate mark-recapture models
Contents:
- 01_installingmarkrecappackages.R checks if required packages are installled. Installs them if they are not.
- 02_markrecaptureworkshopcode.R contains all code used in the workshop
- 03_introduction_to_CJS.R contains code for introduction to Cormack-Jolly-Seber Models
- 04_gof_for_cjs.R contains code for goodness-of-fit tests for Cormack-Jolly Seber Models
- 05_chat_for_cjs.R contains code for estimating variance inflation factor and adjusting model output for Cormack-Jolly-Seber Models
- 06_js_popan.R contains code for estimating population size using Jolly-Seber Models (POPAN formulation)
- 07_knownfate.R contains code for fitting known-fate mark-recapture models with RMark