This codebook.txt file was generated on 20170301 by Hannah S. Specht (with additional information added by Alicia Hofelich Mohr) ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Full simulation data and worked examples from Specht et al. Conditional Occupancy Manuscript 2. Author Information Principal Investigator Contact Information Name: Specht, Hannah S Institution: University of Minnesota Email: spech030@umn.edu Associate or Co-investigator Contact Information Name: Reich, Henry T Associate or Co-investigator Contact Information Name: Iannarilli, Fabiola Associate or Co-investigator Contact Information Name: Edwards, Margaret R Associate or Co-investigator Contact Information Name: Johnson, Michael K Associate or Co-investigator Contact Information Name: Stapleton, Seth P Associate or Co-investigator Contact Information Name: Weegman, Mitch Associate or Co-investigator Contact Information Name: Yohannes, Brittney J Associate or Co-investigator Contact Information Name: Arnold, Todd W 3. Date of data collection (single date, range, approximate date) 2017-02-21 4. Geographic location of data collection (where was data collected?): N/A 5. Information about funding sources that supported the collection of the data: N/A -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: [under review] 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? No If yes, list source(s): 6. Recommended citation for the data: Specht, Hannah S; Reich, Henry T; Iannarilli, Fabiola; Edwards, Margaret R; Johnson, Michael K; Stapleton, Seth P; Weegman, Mitch; Yohannes, Brittney J; Arnold, Todd W. (2017). Full simulation data and worked examples from Specht et al. Conditional Occupancy Manuscript. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/184711. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: AS4_Specht_etal_SimDataSet_metadata.csv Short description: Variable labels for AS4_Specht_etal_SimulationData.csv B. Filename: AS4_Specht_etal_SimulationData.csv Short description: Simulation data generated by Specht_etal_AS3_CondOcc_SimulationCode.R C. Filename: PRESENCE_files_for_Specht_etal.zip Short description: Zip folder containing data and analysis files for analyzing conditional, standard and removal design data in Program PRESENCE. Program PRESENCE can be accessed through Hines, J.E. & Mackenzie, D.I. (2004). Presence. USGS Patuxent Wildlife Research Center, Patuxent, Maryland. URL http://www.mbr-pwrc.usgs.gov/software/presence.html. Provided examples represent the use of each method in a case where true occupancy is 0.2 and true detection probability is 0.5. Occupancy and detection each have a unique, continuous, site-specific covariate (Ag.Cover and Veg.Den, respectively) as well as a shared, continuous, site-specific covariate (Biomass). Provided models include a constant model and a fully parameterized covariate model. This zip file contains three folders with files to run each of the models in PRESENCE: PRESENCE_files_ConditionalOccupancy e420_psi2p5_conditional_sharedcovs.pa3 pres_psi(AgCover_P_Biomass)_p(Biomass_P_VegDen).out e420_psi2p5_conditional_sharedcovs.dm pres_psi(.)_p(.).out e420_psi2p5_conditional_sharedcovs.pao PRESENCE_files_RemovalOccupancy e420_psi2p5_removal_sharedcovs.pa3 e420_psi2p5_removal_sharedcovs.dm pres_psi(AgCovPBiomass)_p(Biomass_PVegDen).out pres_psi(.)_p(.).out e420_psi2p5_removal_sharedcovs.pao PRESENCE_files_StandardOccupancy e420_psi2p5_standard_sharedcovs.pa3 pres_psi(AgCov_P_Biomass)_p(Biomass_P_Vegden).out e420_psi2p5_standard_sharedcovs.dm pres_psi(.)_p(.).out e420_psi2p5_standard_sharedcovs.pao .pao files contain PRESENCE data .pa3 and .out files contain model results .dm files contain the design matrix D. Filename: ProgramMARK_files_for_Specht_etal.zip Short description: Zip folder containing data and analysis files for analyzing conditional, standard and removal design data in Program MARK. Program MARK can be accessed through White, G.C. & Burnham, K.P. (1999). Program MARK: survival estimation from populations of marked animals. Bird Study, 46, S120–S139. Provided examples represent the use of each method in a case where true occupancy is 0.2 and true detection probability is 0.5. Occupancy and detection each have a unique, continuous, site-specific covariate (Ag.Cover and Veg.Den, respectively) as well as a shared, continuous, site-specific covariate (Biomass). Provided models include a constant model and a fully parameterized covariate model. Zip file contains: E420_PSI2P5_CONDITIONAL_SHAREDCOVS.DBF E420_PSI2P5_CONDITIONAL_SHAREDCOVS.FPT E420_psi2p5_Conditional_SharedCovs.inp E420_PSI2P5_REMOVAL_SHAREDCOVS.DBF E420_PSI2P5_REMOVAL_SHAREDCOVS.FPT E420_psi2p5_Removal_SharedCovs.inp E420_PSI2P5_STANDARD_SHAREDCOVS.DBF E420_PSI2P5_STANDARD_SHAREDCOVS.FPT E420_psi2p5_Standard_SharedCovs.inp .DBF files contain the results for each model .FPT files are the memo fields for each model .inp files are the input files for each model E. Filename: Specht_etal_AS3_CondOcc_SimulationCode.R Short description: Code used to generate simulation data in AS4_Specht_etal_SimulationData.csv F. Filename: Unmarked_example_for_Specht_etal.R Short description: Data simulation and analysis script for analyzing conditional, standard and removal design data in R package unmarked. unmarked can be accessed through Fiske, I. & Chandler, R. (2011). unmarked: An R Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance. Journal of Statistical Software. Journal of Statistical Software, 43, 1–23. Provided examples represent the use of each method in a case where true occupancy is 0.2 and true detection probability is 0.5. Occupancy and detection each have a unique, continuous, site-specific covariate (Ag.Cover and Veg.Den, respectively) as well as a shared, continuous, site-specific covariate (Biomass). Provided models include a constant model and a fully parameterized covariate model. 2. Relationship between files: 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. 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? yes/NO Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Manuscript under review 2. Methods for processing the data: AS4_Specht_etal_SimulationData.csv provides raw simulation result data from MCMC analyses used compare the performance of standard, removal and conditional occupancy designs. Data were simulated and subsequently analyzed across true values of occupancy and detection probabilities ranging from 0.1-0.9 by intervals of 0.1, at a range of total efforts (120, 420 and 1500) and maximum visits (3, 5 and 15). The data set includes 100 iterations at each combination. PRESENCE_files_for_Specht_etal.zip, ProgramMARK_files_for_Specht_etal.zip and Unmarked_example_for_Specht_etal.R files provide code for simulating data OR data that were simulated for a case where true occupancy probability was 0.2 and true detection probability was 0.5 under each design (standard, removal, conditional). 3. Instrument- or software-specific information needed to interpret the data: Unmarked_example_for_Specht_etal.R requires R and package unmarked ProgramMARK_files_for_Specht_etal.zip requires Program MARK PRESENCE_files_for_Specht_etal.zip requires Program PRESENCE Specht_etal_AS3_CondOcc_SimulationCode.R requires R, JAGS and R package R2jags R Session information: R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils [5] datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.3 > JAGS: Version 4.1.0 R2jags: Version: 0.5-7 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: N/A 6. Describe any quality-assurance procedures performed on the data: N/A 7. People involved with sample collection, processing, analysis and/or submission: All listed co-authors