DOI: 10.5061/dryad.w0vt4b92h
title: Data from: Under cover: The nuanced influence of functional properties of cover on resource selection by pygmy rabbits (Brachylagus idahoensis)

description: Animals at risk of predation select habitat that enhances security from
 predators. Two properties of cover related to security are concealment
 (i.e., habitat structure that blocks an individual from detection by
 others) and visibility (i.e., visual information accessible relative to
 habitat structure). Although these properties are often negatively
 correlated, they are not always inverse; animals in habitat with
 heterogenous structure maybe be able to select for both. We investigated
 habitat use by pygmy rabbits (Brachylagus idahoensis) at 2 scales (patch
 and microsite) to evaluate the influence of both structural properties of
 cover and visual properties (concealment and visibility) on habitat use by
 prey. We contrasted vegetation structure at paired used and unused
 patches. At each patch, we measured concealment and viewshed (i.e.,
 visibility) in 3 orientations (i.e., aerial, terrestrial, and overall) and
 structural density using lidar. We also measured heights of the 3 tallest
 shrubs. Additionally, within used patches, we assessed the density of
 fecal pellets as an index of intensity of use and also measured distance
 to nearest burrow. At the patch scale, rabbits selected for structural
 properties of cover (dense vegetation and tall shrubs), but not visual
 properties of cover. Pygmy rabbits more intensively used microsites
 associated with high terrestrial concealment and in proximity to burrows.
 Our results suggest that pygmy rabbits may perceive greater threat from
 terrestrial as opposed to aerial predators at both scales, and they also
 indicate a nuanced relationship between properties of cover and habitat
 use.
description: # Under cover: The nuanced influence of functional properties of cover on
 resource selection by pygmy rabbits (Brachylagus idahoensis)
 [https://doi.org/10.5061/dryad.w0vt4b92h](https://doi.org/10.5061/dryad.w0vt4b92h) ## Description of the data and file structure **File Descriptions and Folders:** \- Concealment Photos: Contains all photographs taken for concealment analyses ordered by photo number (DSCN####). Note that not all numbers in the sequence are present because the camera was used for other purposes such as taking photos of the field site \- Scans: Contains all lidar scans used for viewshed analysis. Most are named for the rabbit captured or, in the second year, mounds with evidence of activity (the rabbit numbering scheme continued). R# is the rabbit or mound number, u if the mound was used, nu if the mound was not used, then 1 or 2 or 3 for the position. There are scans from additional used mounds incorporated into the microsite analysis for this project. Those are named with the mound number # then u then 1 or 2 or 3. They do not have an associated unused mound and so were only used in microsite analyses. **Files:** \- Field_Data.xlsx: relevant data gathered in the field \- Animal: assigned ID of captured animal or other used mound \- Year \- Sex: if an animal was captured \- Mass: of captured animal (g) \- Date_collared: date the animal was collared \- date_collar_removed: date the animal's collar was removed \- tag_f: frequency of the collar for tracking \- u_GPS_n: Northing GPS location of used mound \- u_GPS_e: Easting GPS location of used mound \- u_shrub_1/2/3: height (cm) of the three largest shrubs \- u_radius: radius (cm) of used mima mound \- u_1_az: angle from North to position 1 (gathered using a random number generator) \- u_1_dtoc: distance to center from position 1 (generated from a random number generator based on the radius) \- u_2_az: angle from North to position 2 (gathered using a random number generator) \- u_2_dtoc: distance to center from position 2 (generated from a random number generator based on the radius) \- u_3_az: angle from North to position 3 (gathered using a random number generator) \- u_3_dtoc: distance to center from position 3 (generated from a random number generator based on the radius) \- u_1_pellet: number of fecal pellets in position 1 \- u_2_pellet: number of fecal pellets in position 2 \- u_3_pellet: number of fecal pellets in position 3 \- u_c.h.r.: used concealment horizontal reference photo - photo number of unobstructed reference (for use if cropping method not accessible) \- u_c.v.r.: used concealment vertical reference photo - photo number of unobstructed reference photo from above (for use if cropping method not accessible) \- u_#_c.d.: used concealment photo from position # in d direction (n, s, e, w) \- u_#_c.v: used aerial concealment photo from position # \* where nu is in the name rather than u, those data are from the associated unused mound \* because pygmy rabbits are a species of concern and some populations are endangered, we have removed the GPS coordinates from the file \- Additional Field Data: additional relevant data gathered in the field that was incorporated into this project. \- Where there is NA in the used mound data in the Field Data file, those data can be found in this file, look to the notes to identify mounds \- Mound_#: mound number \- GPS_e: Easting coordinates \- GPS_n: Northing coordinates \- Mound_Radius: cm \- Shrub_#: heights of the three tallest shrubs (cm) \- Pellets_P#: number of fecal pellets at each of the three positions \- P#_az: angle from north to position # (generated from a random number generator) \- P#_dtoc: distance to center from position # (generated from a random number generator based on the radius) \- c.h.r.: concealment photo horizontal reference \- c.v.r: concealment photo vertical reference \- P#_c.d.: concealment photo at position # from d direction (n,s,e,w) \_ P#_c.v.: aerial concealment photo from position # \* because pygmy rabbits are a species of concern and some populations are endangered, we have removed the GPS coordinates from the file \- microsites: data associated with each measured microsite on used mounds \- rabbit/mound: mound identification \- pellets: number of fecal pellets \- a_conceal: aerial concealment \- t_conceal: terrestrial concealment (average of concealment in the four cardinal directions) \- overall_conceal: overall concealment (average of concealment in the four directions and aerial concealment) \- overall_vc: overall viewshed coefficient \- overall_cov: overall coefficient of variation of the viewshed \- a_vc: aerial viewshed coeffienct \- a_cov: aerial coefficient of variation of the viewshed \- t_vc: terrestrial viewshed coefficient \- t_cov: terrestrial coefficient of variation of the viewshed \- dt_center: distance from measured position to mound center (cm) \- shrub_#: height of the three tallest shrubs (cm) \- pointsv: number of lidar points in the scan classified as vegetation \- points: number of lidar points in the scan \- mima_mounds: data associated with the microsites on the paired used and available mounds \- animal: mound identification \- mass: mass of animal for those captured and tracked (g) \- s_p#_shrub: height of the three tallest shrubs on the selected (used) mound \- s_radius: radius of the selected (used) mound \- s_p#_dtoc: distance to center from position # to the center of the selected (used) mound \- s_p#_a_conceal: aerial concealment at position # on the selected (used) mound \- s_p#_t_conceal: average terrestrial concealment at position # on the selected (used) mound \- s_p#_overall_conceal: average terrestrial and aerial concealment at position # on the selected (used) mound \- s_p#_a_vc: aerial viewshed coefficient at position # on the selected (used) mound \- s_p#_a_cov: aerial coefficient of variation of the viewshed at position # on the selected (used) mound \- s_p#_t_vc: terrestrial viewshed coefficient at position # on the selected (used) mound \- s_p#_t_cov: terrestrial coefficient of variation of the viewshed at position # on the selected (used) mound \- s_p#_overall_vc: overall viewshed coefficient at position # on the selected (used) mound \- s_p#_overall_cov: overall coefficient of variation of the viewshed at position # on the selected (used) mound \* where a is in the name rather than s, those data are from the associated available (unused) mound ### Files and variables #### File: Scans.zip **Description:** All lidar scans used in the project #### File: Folder\_and\_File\_Descriptions.txt **Description:** Detailed descriptions of all files and naming conventions in the data set **File: Concealment_Photos.zip** **Description:** All concealment sphere photographs used in the project **File: Additional_Field_Data.xlsx** **Description:** Additional field-based data, not associated with captured animals **File: Field_Data.xlsx** **Description:** Field based-data **File: microsites.csv** **Description:** data processed for analyses of microsite use ##### Variables * rabbit/mound: * position: * pellets: * a_conceal: * t_conceal: * overall_conceal: * overall_vc: * overall_cov: * a_vc: * a_cov: * t_vc: * t_cov: * dt_center: * shrub_1: * shrub_2: * shrub_3: * pointsv: * points: **File: mima_mounds.csv** **Description:** data processed for analyses of mima mound selection ##### Variables * animal: * Year: * sex: * mass: * s_p1_shrub: * s_p2_shrub: * s_p3_shrub: * s_radius: * s_p1_dtoc: * s_p2_dtoc: * s_p3_dtoc: * s_p1_a_conceal: * s_p1_t_conceal: * s_p1_overall_conceal: * s_p2_a_conceal: * s_p2_t_conceal: * s_p2_overall_conceal: * s_p3_a_conceal: * s_p3_t_conceal: * s_p3_overall_conceal: * s_p1_a_vc: * s_p1_a_cov: * s_p1_t_vc: * s_p1_t_cov: * s_p1_overall_vc: * s_p1_overall_cov: * s_p2_a_vc: * s_p2_a_cov: * s_p2_t_vc: * s_p2_t_cov: * s_p2_overall_vc: * s_p2_overall_cov: * s_p3_a_vc: * s_p3_a_cov: * s_p3_t_vc: * s_p3_t_cov: * s_p3_overall_vc: * s_p3_overall_cov: * : * a_p1_shrub: * a_p2_shrub: * a_p3_shrub: * a_radius: * a_p1_dtoc: * a_p2_dtoc: * a_p3_dtoc: * a_p1_a_conceal: * a_p1_t_conceal: * a_p1_overall_conceal: * a_p2_a_conceal: * a_p2_t_conceal: * a_p2_overall_conceal: * a_p3_a_conceal: * a_p3_t_conceal: * a_p3_overall_conceal: * a_p1_a_vc: * a_p1_a_cov: * a_p1_t_vc: * a_p1_t_cov: * a_p1_overall_vc: * a_p1_overall_cov: * a_p2_a_vc: * a_p2_a_cov: * a_p2_t_vc: * a_p2_t_cov: * a_p2_overall_vc: * a_p2_overall_cov: * a_p3_a_vc: * a_p3_a_cov: * a_p3_t_vc: * a_p3_t_cov: * a_p3_overall_vc: * a_p3_overall_cov: #### **File: rabbit\_viewsheds.R** **Description:** code for processing lidar scans for viewshed estimation. This script includes the code for measuring the viewshed coefficient as well as the coefficient of variation for overall, aerial, and terrestrial viewsheds within each lidar scan.  ## Code/software Program R is needed to run these data including the following packages: * viewshed3d * lidR * pracma * tidyr * dplyr * ggplot2 * lme4 * trtools * whereami