cbalantic / dynamic-occupancy-acoustic Goto Github PK

This Github repository exists to reproduce the analysis from the following paper:

Balantic, C. M., & Donovan, T. M. (2019). Dynamic wildlife occupancy models using automated acoustic monitoring data. Ecological Applications. DOI: 10.1002/eap.1854 https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/eap.1854

Repository code contained here is identical to the code contained in the Data S1 supplement of the paper. Because Github is not designed for file storage and some of the data files exceed Github's upload limits, files in the "Data" folder listed below are not available on Github and can be obtained from the paper supplement here: Data S1 supplement (WARNING: clicking this link will download a zip folder of the supplement). Note that you can reproduce the .RDS files in the "Data" folder by running the scripts, but the .RDS files are provided in case you wish to skip this step and dig into the code itself.

Content List:

Code [Folder]

• Appendix-S3-Script.R
• Simulation-Functions.R
• Simulation-Script.R

Data [Folder]

• appendix-results [Folder]

  • amdata_object.RDS
  • bias_detection.RDS
  • bias_state.RDS
  • presence_warnings.RDS

• simulation-results [Folder]

  • amdata_object.RDS
  • bias_detection.RDS
  • bias_state.RDS
  • presence_warnings.RDS

Content Description:

Code: folder containing three .R files, all three of which are heavily commented to be followed along with by a user.

• Appendix-S3-Script.R – an R script to replicate the simulation results contained in Appendix S3 (copies of which are provided in the Data folder 'appendix-results').
• Simulation-Functions.R – an R file containing all functions required to run Appendix-S3-Script.R and Simulation-Script.R.
• Simulation-Script.R – an R script to replicate the simulation results contained in the main body of the paper (copies of which are provided in the Data folder 'simulation-results').

Data: folder containing two folders of results

• appendix-results: a folder containing all data produced by the Appendix S3 simulation results (which can be reproduced using Appendix-S3- Script.R)

  • amdata_object.RDS – an RDS file containing an AMModels class ‘amData’ object which stores dynamics, encounter histories, data summaries, and parameter estimates from each of 100 replicates of all 192 appendix simulation scenarios.
  • bias_detection.RDS – an RDS file containing a data.table with dimensions 19,200 x 18 that stores parameter estimates from each of 100 replicates of all 192 appendix simulation scenarios, for the occupancy detection parameters p11, p10, and b. This object is used to produce plots of the bias of detection parameters with the function simBiasPlot() provided in Simulation-Functions.R and used in Appendix-Script.R.
  • bias_state.RDS – an RDS file containing a data.table with dimensions 19,200 x 18 that stores parameter estimates from each of 100 replicates of all 192 appendix simulation scenarios, for the occupancy state parameters psi (ψ), gamma (γ), and epsilon (ε). This object is used to produce plots of the bias of state parameters with the function simBiasPlot() provided in Simulation-Functions.R and used in Appendix-Script.R.
  • presence_warnings.RDS – an RDS file containing a data.table storing the scenario name (‘scenario’) and replicate number (‘rep’) of each scenario-replicate that received a warning during model fitting from the program PRESENCE. The column ‘conv.warning’ tracks whether this scenario-replicate received a convergence warning, and if so, at what value. The ‘VC.warning’ column tracks whether this scenario-replicate received a warning about the variance-covariance matrix. This object is used so that scenario-replicates that failed to converge may be removed from plots of parameter bias with the function simBiasPlot() provided in Simulation-Functions.R and used in Appendix-Script.R.

• simulation-results: a folder containing all data produced by the Appendix S3 simulation results (which can be reproduced using SimulationScript.R)

  • amdata_object.RDS – an RDS file containing an AMModels class ‘amData’ object which stores dynamics, encounter histories, data summaries, and parameter estimates from each of 500 replicates of all 128 simulation scenarios.
  • bias_detection.RDS – an RDS file containing a data.table with dimensions 192,000 x 18 that stores parameter estimates from each of 500 replicates of all 128 simulation scenarios, for the occupancy detection parameters p11, p10, and b. This object is used to produce plots of the bias of detection parameters with the function simBiasPlot() provided in Simulation-Functions.R and used in Simulation-Script.R.
  • bias_state.RDS – an RDS file containing a data.table with dimensions 192,000 x 18 that stores parameter estimates from each of 500 replicates of all 128 simulation scenarios, for the occupancy state parameters psi (ψ), gamma (γ), and epsilon (ε). This object is used to produce plots of the bias of state parameters with the function simBiasPlot() provided in Simulation-Functions.R and used in Simulation-Script.R.
  • presence_warnings.RDS – an RDS file containing a data.table storing the scenario name (‘scenario’) and replicate number (‘rep’) of each scenario-replicate that received a warning during model fitting from the program PRESENCE. The column ‘conv.warning’ tracks whether this scenario-replicate received a convergence warning, and if so, at what value. The ‘VC.warning’ column tracks whether this scenario-replicate received a warning about the variance-covariance matrix. This object is used so that scenario-replicates that failed to converge may be removed from plots of parameter bias with the function simBiasPlot() provided in Simulation-Functions.R and used in Simulation-Script.R.