DOI: 10.5061/dryad.15dv41p7w
title: Data and code from: Estimating red deer (<em>Cervus elaphus</em>) population density using drones in a steep and rugged terrain

description: This dataset includes original data and computer code for "Estimating
 red deer (Cervus elaphus) population density using drones in a steep and
 rugged terrain" (Wildlife Biology, DOI: 10.1002/wlb3.01533). The data
 include counts of red deer (Cervus elaphus) from a double
 observer protocol based on overlapping drone images (from different
 angles). The double observer counts cover 331 sampling sites in Lærdal in
 western Norway. The counts are also associated with covariates for each
 sampling site and time, including several covariates not used in the
 analysis presented in the published paper (see description of variables
 here). Further overviews of the data are provided in
 the Supporting Information accompanying the paper. The dataset is
 part of a comprehensive repository (also available on GitHub) which
 includes scripts for summarizing and transforming data, as well as all
 code for fitting the hierarchical models, using Bayesian MCMC sampling in
 NIMBLE, that are presented in the paper.  
description: # Data and code from: Estimating red deer (*Cervus elaphus*) population
 density using drones in a steep and rugged terrain Dataset DOI:
 [10.5061/dryad.15dv41p7w](10.5061/dryad.15dv41p7w) ## Description of the
 data and file structure Data and computer code for "Estimating red
 deer (*Cervus elaphus*) population density using drones in a steep and
 rugged terrain" ### Files and variables #### File: SiteData.rda
 **Description:** The main data file (see below for the complete archived
 repository including data overviews and computer code). **Variables:** The
 `SiteData.rda` file contains data.frame `SiteData` with the following
 variables: * `Survey`: A single flight conducted using a UAV to collect
 data over a designated area. A total of 31 survey flights were conducted
 in this study. * `Study_area`: A specific geographic location selected for
 conducting surveys. For this study, four sampling areas were selected:
 Haugen, RC%, Sprakehaug, and SC8re BjC8rkum. * `Route`: A predetermined
 flight path followed by the UAV during a survey. In this study, each
 sampling area contained between three and five routes, and each route was
 surveyed between one and three times. * `Month`: The month during which a
 survey was conducted (March or April). * `Date`: The specific date a
 survey was conducted (R Date format). * `Flight_Altitude`: Programmed
 flight altitude above ground in meters, based on the digital elevation
 model. * `Focal_image`: Unique identifier for the focal image constituting
 the `Site`. All focal images are non-overlapping with other focal images
 from the same survey. * `Site`: Site number within `Survey`, numbered
 consecutively from 1 within each `Survey`. * `File`: File name for the
 `Folcal image`. Each file name corresponds to a raster image used for
 extracting information such as mean elevation, distance to the field, etc.
 from a Digital Elevation Model (DEM) (see variables below). * `Weather`:
 The weather conditions during a survey as noted by Yr.no and confirmed by
 observations, such as clear, mostly clear, mostly overcast, mostly sunny,
 overcast, slightly overcast, or sunny. * `Temperature_C`: The temperature
 (in degrees Celsius) at the end of a survey. * `Snow`: Whether the survey
 area was covered with snow during the survey (yes or no). A survey area
 was considered snow-covered if more than 50% of the aerial images
 displayed snow-covered surfaces. * `Area`: The total area (in square
 meters) covered by a site within a focal image. * `mean_x`: The mean UTM
 zone 33V x-coordinate (east) of all pixels within a focal image. *
 `mean_y`: The mean UTM zone 33V y-coordinate (north) of all pixels within
 a focal image. * `elevation_at_mean_pos`: The elevation at the average
 east (x) and north (y) UTM coordinate of the site, derived from a DEM. *
 `mean_elevation`: The average elevation (in meters above sea level) of a
 site, calculated as the mean of all elevation values within the site,
 derived from a DEM. * `min_elevation`: The lowest elevation (in meters
 above sea level) within the site, derived from a DEM. * `max_elevation`:
 The highest elevation (in meters above sea level) within the site, derived
 from a DEM. * `proportion_no_field`: The proportion of the site that does
 not consist of fields. Calculated as the area of non-field land cover
 (e.g., forest, water, bare ground) divided by the total area of the site,
 derived from a polygon file. * `field_dist_at_mean_pos`: The distance (in
 meters) from the average east (x) and north (y) UTM coordinate of the site
 to the nearest field, derived from a DEM and a habitat polygon file. *
 `mean_field_dist`: The average distance (in meters) from all points within
 a site to the nearest field, calculated as the mean of all distance values
 within the site, derived from a DEM and a habitat polygon file. *
 `min_field_dist`: The shortest distance (in meters) from any point within
 a site to the nearest field, derived from a DEM and a habitat polygon
 file. * `max_field_dist`: The longest distance (in meters) from any point
 within a site to the nearest field, derived from a DEM and a habitat
 polygon file. * `proportion_forest`: The proportion of a site that
 consists of forested land, calculated as the area of forest cover divided
 by the total area of the site, derived from a habitat polygon file. *
 `forest_dist_at_mean_pos`: The distance (in meters) from the average east
 (x) and north (y) UTM coordinate of a site to the nearest forested area,
 derived from a DEM and a habitat polygon file. * `mean_forest_dist`: The
 average distance (in meters) from all points within a site to the nearest
 forested area, calculated as the mean of all distance values within the
 site, derived from a DEM and a habitat polygon file. * `min_forest_dist`:
 The shortest distance (in meters) from any point within a site to the
 nearest forested area, derived from a DEM and a habitat polygon file. *
 `max_forest_dist`: The longest distance (in meters) from any point within
 a site to the nearest forested area, derived from a DEM and a habitat
 polygon file. * `aspect_deg`: The average compass direction (in degrees)
 of the slope within a site, calculated as the mean of all aspect values
 within the site, derived from a DEM. Aspect is measured as degree north
 from 0B0 to 360B0, where 0B0 represents north, 90B0 represents east, 180B0
 represents south, and 270B0 represents west. * `slope_deg`: The average
 steepness (in degrees) of the terrain within a site, calculated as the
 mean of all slope values within the site, derived from a DEM. Slope
 represents the angle between the ground surface and a horizontal plane,
 with 0B0 indicating flat terrain and higher values indicating steeper
 slopes. * `n_both`: The number of red deer detected by both observer 1 and
 observer 2 within the site. * `n_only_ab`: The number of red deer detected
 only by observer 1 within the site. * `n_only_jb`: The number of red deer
 detected only by observer 2 within the site. #### File: SuppInfo.html
 (Zenodo - Supplemental information) **Description:** Supplemental
 Information accompanying the paper. #### File: dronedeer-main.zip (Zenodo
 - Software) **Description:** Data and computer code for analysis. This is
 an archived version of the GitHub repository
 [https://github.com/torbjore/dronedeer](https://github.com/torbjore/dronedeer). See the 'README.md' or 'README.html' in the root directory for content of the sub-directories. For a detailed description of the original data file with its variables, see 'data\SiteDataInfo.html' (also available [here](https://torbjore.github.io/dronedeer/SiteDataInfo.html)). Data overviews are given in the [Supporting Information](https://torbjore.github.io/dronedeer/) accompanying the paper (Quarto source code included in the repository under 'Supplemental_Info'). #### File: Deer_drone-master.zip (Zenodo - Software) **Description:** Collection of tools used to map drone images to digital elevation models (DEMs) with no prior photogrammetric processing. See the 'README.md' in the zip-archive - also available on GitHub at [https://github.com/ArcticSnow/Deer_drone](https://github.com/ArcticSnow/Deer_drone).  ## Code/software R (version 4.5.1), NIMBLE (R package version 1.3.0), Quarto (version 1.6.42), and Python (version 3.7) ## Access information Other publicly accessible locations of the data: * [https://github.com/torbjore/dronedeer](https://github.com/torbjore/dronedeer)