Data for fitting spatial capture-recapture (SCR) models to estimate spatially explicit demographics of Mojave desert tortoises on a demography plot in California, USA
Data files
Dec 05, 2025 version files 22.76 KB
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ChinaLake_Detections_SexAge.txt
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ChinaLake_Detectors_Cat.txt
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README.md
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Abstract
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.
Dataset DOI: 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). 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 <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.
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).