Dataset and Code: Evaluating study design and spatial mark-recapture analysis methods for feral cat population monitoring

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This file was created on 2026-06-04 by Annalie Dorph _____________________________ ---- GENERAL INFORMATION ---- _____________________________ Title of dataset: Evaluating study design and spatial mark-recapture analysis methods for feral cat population monitoring Principal Investigator: Dr Annalie Dorph, University of New England, [email protected] Date of data collection: 2023-07 to 2023-09 Geographic location of data collection: Guy Fawkes River National Park, NSW, Australia ______________________________ ---- DATA & FILE OVERVIEW ---- ______________________________ Folder: "code/rt_cat_SMR/" contains all files associated with running the analysis for the Bayesian categorical random-thinning spatial-mark-resight analysis - "./models/" : Folder containing all Bayesian models tested in the analy - "main.R" : A file loads and sets up the data, then runs the analysis - "model_summaries.R" : A secondary file to extract the results of the analysis and summarise the data - "nimble_functions.R" : Custom nimbleFunctions to fit categorical Random Thinning Model. Edited from code provided in doi: 10.1002/eap.2790 - "nimble_restart_MCMC.R" : From code provided in doi: 10.1002/eap.2790 - "overdispersion_check.R" : Code to calculate rudimentary checks of overdisperion within datasets - "prepare_camera_data.R" : A function to take raw camera data extracts and create a list of outputs for the function "prepare_nimble_data.R". Requires the following: * Camera locations : A csv with the columns CameraCode, Longitude, Latitude * Camera operation data : A csv with columns Camera, Date, Status for every day cameras were deployed. Status column contains "working"/"not working". * Camera data extract : A csv with columns Camera, DateTimeOriginal, FinalID (a name for individuals, or NO_FINAL_ID), Bicolor (contains Y/N), sex (contains MALE/FEMALE), Coat (contains BLACK/WHITE_IR/GING_D/CLAS_TABBY/MACK_TABBY/TORT), Long_Hair (contains Y/N). - "prepare_nimble_data.R" : A function that takes the output from "prepare_camera_data.R" and creates a list of outputs to use in the Bayesian modelling. - "run_nimble_model.R" : A function to take the outputs from "prepare_camera_data.R", "prepare_nimble_data.R", and a model script from the "./models/" folder to run the Bayesian models. Folder: "data_edited/rt_cat_SMR/" contains all file outputs from "code/rt_cat_SMR/prepare_camera_data.R" and "./prepare_nimble_data.R" Folder: "code/secr_SMR/" contains all files associated with running the analysis for the maximum likelihood SMR analysis - "main.R" : A file loads and sets up the data, runs the analysis and extracts the estimates - "prepare_camera_data.R" : A function to take raw camera data extracts and create several outputs for the models. Requires the following: * Camera locations : A csv with the columns CameraCode, Longitude, Latitude * Camera operation data : A csv with columns Camera, Date, Status for every day cameras were deployed. Status column contains "working"/"not working". * Camera data extract : A csv with columns Camera, DateTimeOriginal, FinalID (a name for individuals, or NO_FINAL_ID), Bicolor (contains Y/N), sex (contains MALE/FEMALE), Coat (contains BLACK/WHITE_IR/GING_D/CLAS_TABBY/MACK_TABBY/TORT), Long_Hair (contains Y/N). - "run_secr_model.R" : A function that takes the output from "prepare_camera_data.R" and builds SMR models. Folder: "data_edited/secr_SMR/" contains all the file outputs from "code/secr_SMR/prepare_camera_data.R".