Updated 2025-04-25 ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: R Code and Output Supporting: Modeling individual variability in habitat selection and movement using integrated step-selection analyses 2. Author Information: Name: Nilanjan Chatterjee Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: nchatter@umn.edu Name: David Wolfson Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: wolfs064@umn.edu Name: Dongming Kim Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: kimx3725@umn.edu Name:Juliana Velez Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: julianavelezgomez@gmail.com Name: Smith Freeman Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: freem850@umn.edu Name: Nathan M. Bacheler Affiliation: Southeast Fisheries Science Center, National Marine Fisheries Service, Beaufort, NC 28516, USA. Email: nate.bacheler@noaa.gov Name: Kyle Shertzer Affiliation: Southeast Fisheries Science Center, National Marine Fisheries Service, Beaufort, NC 28516, USA. Email: kyle.shertzer@noaa.gov Name: J. Christopher Taylor Affiliation: National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic and Atmospheric Administration,Beaufort, NC 28516, U.S. Email: chris.taylor@noaa.gov Name: John R. Fieberg Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: jfieberg@umn.edu 3. Overview of the data and files: This repository contains R code and associated output supporting the results reported in: Chatterjee, N., Wolfson, D., Kim, D., Velez, J., Freeman, S., Bacheler, N. M., Shertzer, K.,Taylor, J. C., and Fieberg, J. 2023. Modeling individual variability in habitat selection and movement using integrated step-selection analyses. Methods in Ecology and Evolution. https://doi.org/10.1101/2023.07.31.551213 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data and code: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: Chatterjee, N., Wolfson, D., Kim, D., Velez, J., Freeman, S., Bacheler, N. M., Shertzer, K.,Taylor, J. C., and Fieberg, J. 2023. Modeling individual variability in habitat selection and movement using integrated step-selection analyses. Methods in Ecology and Evolution. 3. Recommended citation for this archive: Chatterjee, N., Wolfson, D., Kim, D., Velez, J., Freeman, S., Bacheler, N. M., Shertzer, K.,Taylor, J. C., and Fieberg, J. 2023. R Code and Output Supporting: Modeling individual variability in habitat selection and movement using integrated step-selection analyses. University of Minnesota Digital Conservancy. https://doi.org/10.13020/27hq-zx30 --------------------- FILE OVERVIEW --------------------- 1. A. Filename: Snapper_final_data_6min.rds Short description: Dataset used for the integrated step-selection analysis (465903X12) column name: "id" - id of the individual fish "burst_" - burst number for individual fish "sl_" - Step-lengths between consecutive fixes "ta_" - Relative turn-angle between three consecutive fixes "dt_" - Time difference in mins "case_" - FALSE/TRUE if the step is available or used "log_sl_" - Log(step-length) mentioned earlier "cos_ta_" - Cosine(relative turn-angle) "step_id" - Unique individualX step_id for the random effect modelling "reefS4" - Reef habitat for the end of the step (0/1 for hardbottom or sand habitat) "reefE4" - Reef habitat for the start of the step (0/1 for hardbottom or sand habitat) "newdist" - Distance from the closest reef B. Filename: Move_simulation_final.html Short description: html file containing R code and output from running the codes; a tutorial demonstrating how to do the simulation modelling to understand difference between individual modelling vs mixed-effect models. C. Filename: mixedssa_vignette.pdf A vignette of the R package "mixedSSA" with the ISSA dataset of red snappers provided here. D. Filename: Move_simulation_final_vignette.R Short description: R file that containing the code underlying Move_simulation_final.html Addition files appended 2025-04-25 "The mixedSSA R package referenced in the DRUM repository has been updated, and we have identified a mistake in one of the equations in the appendix. We have contacted the journal and submitted an erratum, and they have also requested that we update the associated supporting documents." E. Update_delta_method.html Short description: A rendered (knitted) HTML file that includes R code and explanations for using the delta method to estimate functions of movement parameters. This file was used to produce the updated version of Figure 5 from the manuscript. F. Update_delta_method.R Short description: The raw R script corresponding to Update_delta_method.html. It contains the underlying code used in the delta method calculations. G. helper_functions.R Short description: A script containing custom helper functions that are sourced and used across the R scripts listed above. These functions support model fitting, and handling of result output. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Methods: For complete methodological details, please refer to Chatterjee et al. (2023). 2. Instrument- or software-specific information needed to interpret the data: Programs were written for Program R (R Core Team 2020) and full session information, including packages used, are provided at the bottom of each example.html file. Note: the input used for the integrated step-selection analysis can be found in the file "Snapper_final_data_6min.rds". The code and output for the simulation are provided in the "Move_simulation_final.html" file. The code to replicate the analysis using the empirical data can be found in the "mixedssa_vignette.pdf".