Intraspecific encounters can induce home-range shifts: Associated R Scripts

Zenodo archive v1.0.0 (for initial review/preprint)

Authors: William F. Fagan^1,*, Ananke Krishnan^1§, Qianru Liao^1§, Christen H. Fleming^1,2,3, Daisy Liao¹, Clayton Lamb⁴, Brent Patterson⁵, Tyler Wheeldon⁵, Ricardo Martinez-Garcia^3,6, Jorge F. S. Menezes³, Michael J. Noonan⁷, Eliezer Gurarie⁸, and Justin M. Calabrese^1,3,9

¹Department of Biology, University of Maryland, College Park, MD, United States

²Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, United States

³Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rosendorf (HZDR), Görlitz, Germany

⁴Department of Biology, University of British Columbia, Kelowna, BC, Canada

⁵Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON, Canada

⁶ICTP - South American Institute for Fundamental Research & Instituto de Física Teórica, Universidade Estadual Paulista - UNESP, São Paulo, SP, Brazil.

⁷Department of Biology, The University of British Columbia Okanagan, Kelowna, BC, Canada

⁸Department of Environmental Biology, SUNY Environmental Science and Forestry, Syracuse, NY, United States

⁹Department of Ecological Modelling, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany

^*Correspondence Author

^§Joint Second Authors

This repo contains the code and additional data required to reproduce the results in this manuscript. More detail on each file is provided below:

R Files

• encounter_homeranges.R: Code to calculate home range shifts before and after the encounter for both individuals involved in encounter. Used to generate data for Fig. 1A-D.
• encounter_bls.R: Code to calculate ballistic length scale over sliding windows for a single individual. Used to generate data for Fig. 1E.
• encounter_bears.R: Code to calculate home range shifts for bears and run population level comparisons on individuals' home ranges before and after encounters. Used to generate data for Fig. 2.
• supplementalfigs.R: Code to generate supplemental figures from data files (code to generate data files shown in encounter_bears.R). Fig. S3 waiting on some data owner permission.

Data Files

• bearpairsto500m.csv: all pairs that came within up to 500m of each other (n=103, n_kept due to data quality = 77). Columns are as follows:

  • bear#1: individual 1
  • bear#2: individual 2
  • time: year-month-day hour-minute-second of encounter
  • low, est, high: minimum distance between individuals at encounter (in meters)
  • trackstart: beginning of overall track for both individuals
  • trackstop: ending of overall track for both individuals.

• bd_reloverlap_500m.csv: population-level overlap between home ranges after encounters up to 500m, bhattacharyya distance and percent of the overlap of home ranges before encounter.

  • subset: describes selected group of individuals (all encounters, encounters btwn same sex individuals, encounters btwn diff sex individuals, encounters in late fall, encounters in spring, encounters btwn diff sex individuals in late fall)
  • threshold: category for how close the encounters were (50m, 100m, 200m, 300m, 400m, 500m)
  • p: p-val indicating whether the before/ after population-level overlap shifts are significantly different
  • before_bd_low, est, high: low, est, high meta bhattacharyya distance between home ranges before encounter
  • after_bd_low, est, high: low, est, high meta bhattacharyya distance between home ranges after encounter
  • rel_overlap_low, est, high: low, est, high meta percent overlap (after/before encounter)

• uds_btwninds.csv: UDS percent overlap for each individual in pair before and after all encounters (n=103, n_kept due to data quality = 77). Shows change between overlap of both individuals' home ranges before and after encounter.

• uds_withininds.csv: UDS percent overlap for each individual in pair before and after encounters up to 100m (n=44, n_kept due to data quality = 32) . Shows change within overlap of individual home ranges for each individual in pair before and after encounter.

Additional notes:

• All encounters with any subsets with an ESS <2 were dropped due to data quality concerns. All encounters with subsets with 2 < ESS < 5 were bootstrapped with ctmm.boot.
• Some of the analyses require meta information on cubs/encounter. This information is still protected and will be released following data owner permission.

*Movement data is available on Movebank.org data as datasets 1614661371 (coyotes) and 1044288582 (grizzly bears).