DOI: 10.5061/dryad.k98sf7mk4
title: Data for fitting spatial capture-recapture (SCR) models to estimate spatially explicit demographics of Mojave desert tortoises on a demography plot in California, USA

description: These data are comprised of input files formatted for fitting spatial
 capture-recapture (SCR) models to estimate Mojave desert tortoise
 (Gopherus agassizii) density and sex by size class compositions on a
 previously unsampled demography plot in the Mojave Desert in California,
 USA. Data were collected during capture-mark-recapture surveys to identify
 tortoise sign on a 1-km2 plot within the South Range of U.S. Department of
 Navy - Naval Air Weapons Station China Lake (NAWSCL). Surveys were
 conducted over four days during September 2022. Data were collected as
 part of a study to estimate tortoise population demographics over time on
 NAWSCL.
description: Data were collected from mark-recapture Mojave desert tortoise
 (Gopherus agassizii) demographic plot surveys within a previously
 unsampled 1-kilometer x 1-kilometer area over four days in September 2022
 within the south range of U.S. Department of Navy - Naval Air Weapons
 Station China Lake, California, USA. During surveys, all tortoise signs
 (e.g. live tortoises, carcasses, and scat) were recorded by surveyors
 walking transects. In addition, surveyors recorded their daily survey
 tracks using a global positioning system (GPS) units. All tortoise
 detection data from 25 tortoises were converted to three-dimensional
 spatially explicit detection histories and plotted with surveyors’ GPS
 tracks to discretize a continuous grid of ‘effective detectors’
 encompassing all tortoise detections and tracks. Two detection data files
 were formatted for fitting spatial capture-recapture (SCR) models to
 estimate Mojave desert tortoise (Gopherus agassizii) density and sex by
 size class compositions of the plot site. Tortoise detection data are
 organized by plot identity, tortoise identity, occasion (day of detection
 during surveys), trap (specific grid cell where tortoise was detected),
 location (tortoise location recorded upon detection), sex (female, male,
 juvenile, or unknown), age (adult or juvenile), and sex by age (female
 adult, male adult, juvenile, unknown adult). Detector data are organized
 by trap (grid cell identity from discretized grid of effective detectors),
 x (UTM Easting of trap), y (UTM Northing of trap), and effort
 (occasion-specific surveyor search effort). 
description: Dataset DOI: [10.5061/dryad.k98sf7mk4](10.5061/dryad.k98sf7mk4) Detection
 data for fitting spatial capture-recapture (SCR) models to estimate
 spatially-explicit demographics of Mojave desert tortoises on a demography
 plot in California, USA. ## Description of the data and file structure
 These data are comprised of input files formatted for fitting spatial
 capture-recapture (SCR) models to estimate Mojave desert tortoise
 (Gopherus agassizii) density and sex by size class compositions on a
 previously unsampled demography plot in the Mojave Desert in California,
 USA. -ChinaLake_Detections_2022_All.txt -ChinaLake_Detectors_Cat.txt These
 data are formatted for fitting spatial capture-recapture models using the
 secr package in basic R, version 4.5.8 ([GitHub - MurrayEfford/secr: R
 package for Spatial Capture-Recapture
 Models](https://cran.r-project.org/package=secr)). Descriptions of
 variables are provided below: **ChinaLake_Detections_SexAge.txt** Tortoise
 detection data are organized by plot identity, tortoise identity, occasion
 (day of detection during surveys), trap (specific grid cell where tortoise
 was detected), location (tortoise location recorded upon detection), sex
 (female, male, juvenile, or unknown), age (adult or juvenile), and sex by
 age (female adult, male adult, juvenile, unknown adult). Session -
 Categorical alphanumeric identifier for the survey plot. The SR prefix
 denotes the Naval Air Weapons Station China Lake South Range. This session
 was the same for all records. ID - Unique alphanumeric identifier for each
 tortoise encountered during the plot survey. These identifiers were
 approved by the United States Fish and Wildlife Service and also attached
 as a paper tag to each tortoise's carapace as able. The identifiers
 included a prefix “CL” denoting the site it was found (China Lake),
 followed by a unique four-digit number. Tortoises that did receive a tag
 (i.e. could not be retrieved to process) would be assigned a temporary
 identifier including a prefix “CL” followed by "temp” and a
 three-digit number. Occasion - Day (1, 2, 3, or 4) of survey of plot SR1
 that tortoise was detected. Trap - Numerical identifier for specific
 discretized grid cell ('effective detector') within which a
 tortoise was detected. Location - Categorical identifier of location of
 tortoise at time of detection; Burrow - tortoise was located in a thermal
 refugia greater than or equal to 1 foot deep, or greater than 50% of the
 tortoise was inside the entrance; Mouth - tortoise was located on the
 apron the burrow, or within 2 feet of the mouth of the burrow, or with
 greater than or equal to 50% of its body outside the entrance; Open -
 tortoise was located on the surface and not directly under cover or within
 shade of vegetation; Veg - tortoise was located directly beneath any part
 of a perennial plant, alive or dead, or in the open but actively using the
 shade of vegetation. Sex - Categorical identifier of sex of tortoise at
 detection: M - male; F - female;U - tortoise sex is unknown. Age -
 Categorical identifier of age of tortoise at detection: A - adult; J -
 juvenile. All tortoises sexed as male, female, or unknown but measured
 ≥180 millimeters of midline carapace length were classified as adults. All
 tortoises sexed as juveniles or unknown but measured &lt;180 millimeters
 of midline carapace length were classified as juveniles. SexAge –
 Categorical identifier of sex by age class of tortoise at detection, which
 combines the Sex and Age variables: FA – female adult; MA – male adult; J
 – juvenile; NA – unknown sex adult. **ChinaLake_Detectors_Cat.txt**
 Detector data are organized by trap (grid cell identity from discretized
 grid of effective detectors), x (UTM Easting of trap), y (UTM Northing of
 trap), and effort (occasion-specific surveyor search effort)). Trap -
 Numerical identifier for specific discretized grid cell that served as an
 'effective detector' within which occasion-specific surveyor
 search effort (meters walked) was assigned and therefore where a tortoise
 could have been detected. X - Easting (Datum: UTM NAD83 11N) location of
 the centroid of each discretized grid cell. Y - Northing (Datum: UTM NAD83
 11N) location of the centroid of each discretized grid cell. Effort -
 Occasion-specific search effort within each ‘effective detector’ that
 surveyors walked to detect tortoises.