Full Simulation Data and Worked Examples from Specht et al. Conditional Occupancy Manuscript

Specht, Hannah SIannarilli, FabiolaEdwards, Margaret RJohnson, Michael KStapleton, Seth PWeegman, MitchYohannes, Brittney JArnold, Todd WReich, Henry T2017-02-272017-02-272017-02-27https://hdl.handle.net/11299/184711To accompany publication of the conditional design for occupancy analysis, we provide the full simulation dataset used to compare the performance of standard, removal and conditional designs in common occupancy analysis programs: R package unmarked, Program MARK and PRESENCE. Specht_etal_AS3_CondOcc_SimulationCode.R is an R script that was used to generate the simulation data in AS4_Specht_etal_SimulationData.csv. AS4_Specht_etal_SimDataSet_metadata.csv contains variable labels for columns in AS4_Specht_etal_SimulationData.csv, including additional calculated variables not generated from the simulations. PRESENCE_files_for_Specht_etal.zip, ProgramMARK_files_for_Specht_etal.zip and Unmarked_example_for_Specht_etal.R provide files to work through examples of conditional, standard and removal occupancy designs for the same case in Program MARK, Program PRESENCE and R package unmarked, respectively. These files allow users to compare estimation by each method in a case where true occupancy probability is 0.2 and true detection probability is 0.5, and provide examples of formatted data input files. See Readme_Specht_etal.txt for more details.Occupancy models are widely used to describe the distribution of rare and cryptic species— those that occur on only a portion of the landscape and cannot be detected reliably during a single survey. However, occupancy models often provide inaccurate estimates of occupancy (ψ ̂) and detection probabilities (p ̂) under these circumstances. We developed a new "conditional" occupancy design that more accurately estimates occupancy for rare species. Here we provide the full simulation dataset used to compare estimation properties of standard, removal and conditional designs. Data were simulated in R and analyzed using MCMC methods in package R2jags. See Specht et al. (in review) for description of methods. Please cite Specht et al. in further use of this data set.Attribution-NonCommercial-ShareAlike 3.0 United Stateshttps://creativecommons.org/licenses/by-nc-sa/3.0/us/rareconditionalremovalspecies occurrencesimulationR2jagsoccupancy modelsFull Simulation Data and Worked Examples from Specht et al. Conditional Occupancy ManuscriptDatasethttps://doi.org/10.13020/D6BS3K