Data and code for "Mt or not Mt: Temporal variation in detection probability in spatial capture-recapture and occupancy models", Sollmann, R., Peer Community Journal (2024)

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DOI (submitted pre-print): https://doi.org/10.1101/2023.08.08.552394

URL (PCJ publication): https://peercommunityjournal.org/articles/10.24072/pcjournal.357/

All code necessary to implement the simulation and case studies described in the above manuscript

Description of the data and file structure

This repository contains the following code files (in folder R) :

Occu simulation all scenarios.R: R code to generate occupancy data and analyze them under a model that does and one that does not account for temporal variation in detection

Occupancy case study MHB.R: R code to repeat occupancy case study for 10 breeding birds from Switzerland

SCR case study brown tree snakes.R: R code to repeat SCR case study for brown tree snakes

SCR case study data prep.R: R code to format original brown tree snake data for secr analysis; no need to run this script as its output is available in data-raw

secr simulation all scenario random Z.R: R code to generate SCR data and analyze them under a model that does and one that does not account for temporal variation in detection

Summarize occu simulations.R: R code to summarize occupancy simulation output and create main Figure 2 and some appendix figures

Summarize secr sim all scenarios.R: R code to summarize SCR simulation output and create main Figure 1 and some appendix figures

Helper functions.txt: R code for two functions, to calculate distances between two sets of coordinates (e2dist) and to generate correlated variables (spcov2)

This repository contains the following data files (in folder data-raw) :

Snake_secr_data.rds: Brown tree snake capture data formatted for secr analysis (original data from Amburgey et al., 2021a; original analysis of the data: Amburgey et al., 2021b)

Sharing/Access information

NA

Code/Software

Simulations require packages secr (Efford, 2022) and unmarked (Fiske and Chandler, 2011). Dataset for occupancy case studies comes with R packages AHMbook (Kéry et al., 2022). Please see R scripts for additional packages used in processing data.

References

Efford MG (2022) secr: Spatially explicit capture-recapture models. R package version 4.5.6. https://CRAN.R-project.org/package=secr

Fiske I, Chandler R (2011) Unmarked: an R package for fitting hierarchical models of wildlife occurrence and abundance. Journal of Statistical Software, 43, 1–23. https://doi.org/10.18637/jss.v043.i10

Kéry M, Royle JA, Meredith M (2022) AHMbook: Functions and Data for the Book “Applied Hierarchical Modeling in Ecology” Vols 1 and 2. R package version 0.2.6. https://CRAN.R-project.org/package=AHMbook

Amburgey, S.M., Lardner, B., Knox, A.J., Converse, S.J., and A.A. Yackel Adams, 2021a, Brown Treesnake detections on transects using potential attractants of live-mouse lures or fish-spray scent, Guam: U.S. Geological Survey data release, https://doi.org/10.5066/P9G6JHZ3.

Amburgey SM, AA Yackel Adams, B Gardner, B Lardner, AJ Knox, and SJ Converse. 2021b. Tools for increasing visual encounter probabilities for invasive species removal: a case study of brown treesnakes. Neobiota 70:107-122. https://doi.org/10.3897/neobiota.70.71379