------------------- GENERAL INFORMATION ------------------- 1. Title: R Code and Output Supporting: A 'How-to' Guide for Interpreting Parameters in Habitat-Selection Analyses 2. Author Information: Name: John R. Fieberg Affiliation: Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota-Twin Cities Email: jfieberg@umn.edu Name: Johannes Signer Affiliation: Wildlife Sciences, Faculty of Forest Science and Forest Ecology, University of Göttingen, Büsgenweg 3, 37077 Göttingen Germany Email: jsigner@gwdg.de Name: Brian Smith Affiliation: Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84322 Email: bjsmith@aggiemail.usu.edu Name: Tal Avgartal Affiliation: Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84322 Email: tal.avgar@usu.edu 3. Description: This repository contains R code and associated output supporting the results reported in: Fieberg, J., Signer, J. 2021. A 'How-to' Guide for Interpreting Parameters in Habitat-Selection Analyses. Journal of Animal Ecology. -------------------------- 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: Fieberg, J., J. Signer, B. Smith, and T. Avgar. 2021. A 'How-to' Guide for Interpreting Parameters in Habitat-Selection Analyses. Journal of Animal Ecology. 3. Links to other publicly accessible locations of the data: The fisher data are available from Movebank: https://www.datarepository.movebank.org/handle/10255/move.330 and were originally described in LaPoint et al. (2013). These data, and also the environmental data, are available in the amt package (Signer et al. 2019). The data usage is permitted for exploratory purposes. For other purposes please get in contact (Scott LaPoint, sdlapoint@gmail.com). LaPoint, S, Gallery P, Wikelski M, Kays R (2013) Animal behavior, cost-based corridor models, and real corridors. Landscape Ecology, v 28 i 8, p 1615–1630. doi:10.1007/s10980-013-9910-0 Movebank data package: LaPoint S, Gallery P, Wikelski M, Kays R (2013) Data from: Animal behavior, cost-based corridor models, and real corridors. Movebank Data Repository. doi:10.5441/001/1.2tp2j43g 4. Recommended citation for this archive: Fieberg, J., J. Signer, B. Smith, and T. Avgar. 2021. R Code and Output Supporting: A 'How-to' Guide for Interpreting Parameters in Habitat-Selection Analyses. University of Minnesota Digital Conservancy. https://doi.org/10.13020/2q0q-yq05 --------------------- FILE OVERVIEW --------------------- 1. fisher_data.csv = fisher location data collected by LaPoint et al. (2013). 2. pop_den.tif = raster with population density (Center for International Earth Science Information Network (CIESIN) Columbia University, & CIAT, Centro Internacional de Agricultura Tropical 2005). 3. landuse.tif = raster with landuse data (Defourny et al. 2009). 4. elevation data = raster with the elevation data (U. S. / Japan ASTER Science Team. 2009). 5. AppA_HSF_examples.R and AppA_HSF_examples.html = R code (and associated html file containing output from running the code); a tutorial demonstrating how to fit and interpret parameters in habitat-selection functions. 6. AppB_SSF_examples.R and AppB_SSF_examples.html = R code (and associated html file containing output from running the code); a tutorial demonstrating how to fit and interpret parameters and output when conducting an integrated step-selection analysis. 7. AppC_iSSA_movement.html = a description of methods used to adjust ‘tentative’ parameters in step-length and turn-angle distributions for the effects of habitat selection when conducting an integrated step-selection analysis. 45 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Methods: For complete methodological details, please refer to Fieberg et al. (2021). 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 fisher, population density, elevation, and landuse data are all contained in the amt package of the R programming language (Signer et al. 2019). Alternatively, the following code could be used to read in these data when working through AppA_HSF_examples.R and AppB_SSF_examples.R: library(amt) library(raster) library(lubridate) fisher <- read.csv("fisher_data.csv") landuse <- raster("landuse.tif") elevation <- raster("elevation.tif") popden <- raster("popden.tif") # parse date fisher$t_ <- ymd_hms(fisher$t_) fisher <- make_track(fisher, x_, y_, t_, id = id, name = name, sex = sex, crs = 5070) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: fisher_data.csv ----------------------------------------- Number of variables: 6 Number of cases/rows: 14230 Variable List A. x_ = longitude of the location B. y_ = latitude of the location C. t_ = date and time of animal location D. sex = sex of the animal E. id = identifier for animal F. name = name of the animal The coordinate reference system is NAD83 (epsg 5070). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: popden.tif ----------------------------------------- Number of rows: 18 Number of columns: 19 Resolution x: 659 Resolution y: 905 The coordinate reference system is NAD83 (epsg 5070). Units are in meters. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: landuse.tif ----------------------------------------- Number of rows: 54 Number of columns: 59 Resolution x: 220 Resolution y: 302 The coordinate reference system is NAD83 (epsg 5070). Units are in meters. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: elevation.tif ----------------------------------------- Number of rows: 272 Number of columns: 294 Resolution x: 44.81 Resolution y: 157.52 The coordinate reference system is NAD83 (epsg 5070). Units are in meters. ----------------------------------------- REFERENCES ----------------------------------------- Center for International Earth Science Information Network (CIESIN) Columbia University, & CIAT, Centro Internacional de Agricultura Tropical. (2005, 20190227). Gridded population of the world, version 3 (gpwv3): Population density grid. Palisades, NY: NASA Socioeconomic Data; Applications Center (SEDAC). Retrieved from https://doi.org/10.7927/H4XK8CG2. Defourny, P., Schouten, L., Bartalev, S., Bontemps, S., Cacetta, P., De Wit, A., . . . others. (2009) Accuracy assessment of a 300 m global land cover map: The GlobCover Experience. LaPoint, S., Gallery, P., Wikelski, M. & Kays, R. (2013). Animal behavior, cost-based corridor models, and real corridors. Landscape Ecology, 28, 1615-1630. R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/. Signer, J., Fieberg, J., & Avgar, T. (2019). Animal movement tools (amt): R package for managing tracking data and conducting habitat selection analyses. Ecology and evolution, 9(2), 880-890. U. S. / Japan ASTER Science Team. (2009). ASTER global digital elevation model data set. NASA eosdis land processes daac. https://lpdaac.usgs.gov/dataset_discovery/aster/aster_products_table/astgtm_v002. doi:10.5067/ASTER/ASTGTM.002