A workshop on occupancy models in R. This workshop uses the 'unmarked', 'RPresence', and 'jagsUI' packages to construct occupancy models in R. All examples use included simulated datasets.
This workshop covers:
- single season occupancy models and goodness-of-fit tests
- building and comparing multiple models
- model-averaging predictions for occupancy models
- fitting dynamic (multi-season) occupancy models
- fitting implicit dynamics occupancy models
- fitting multi-species occupancy models with JAGS
- fitting multi-species occupancy models with covariates and estimating species richness
- fitting multi-species occupancy models estimating the number of undetected species
Contents:
- 01_installingoccupancypackages.R checks if required packages are installled. Installs them if they are not.
- 02_singleseasonoccupancy.R contains code for introduction to occupancy models
- 03_singleseasonoccupancy_part2_modelcomparison.R contains code for building and comparing single season occupancy models
- 04_dynamicoccupancy.R contains code for building dynamic (multi-season) occupancy models
- 05_implicitdynamicsoccupancy.R contains code for building implicit dynamic occupancy models
- 06_multispeciesoccupancy.R contains code for building basic multi-species occupancy models with JAGS
- 07_multispeciesoccupancycovariates.R contains code for multi-species occupancy models with covariates and estimating species richness
- 08_msomundetectedspecies contains code for multi-species occupancy models estimating the number of undetected species
- detection_history.csv contains simulated detection history data
- community_detection_history.RData contains simulated community detection data for 18 species
- community_detection_history_covariates.RData contains simulated community detection data for 18 species for covariate tutorial
- community_detection_3visits.csv contains simulated detection history of 18 species for 3 visits for tutorial estimating undetected species
- site_cov.csv contains simulated site covariates (forest cover and agriculture cover)
- effort.csv contains simulated observation covariate for search effort per survey
- observers.csv contains simulated observation covariate for number of observers per survey
- dynamic_detection_history.csv contains simulated detection history data used in 04_dynamicoccupancy
- dynamic_site_cov.csv contains simulated site covariates (wetland, temp, prec) used in 04_dynamicoccupancy
- dynamic_effort.csv contains simulated observation covariate for search effort per survey used in 04_dynamicoccupancy