https://doi.org/10.5061/dryad.jh9w0vtk2

This dataset contains the various data files and R scripts utilized in the manuscript entitled 'Assessing the suitability of a one-time sampling event for close-kin mark-recapture: A caribou case study.'

Description of the data and file structure

Capture_History_2006-2015.csv - This file contains the capture record for each sample, as uniquely identified by the PCID (2nd column). Samples with the same Cluster_ID (1st column) represent samples from the same individual caribou -- the only exception to this are Cluster_ID of 0, these represent unique singletons (unique individuals for which there is only a single sample). Columns 2-28 represent capture occasions. Column 29 contains the numeric population assignment code, and column 30 contains the sex of each sample (1=female, 2=male, 0=unknown).

Multilocus_Genotypes.csv - This file contains the multilocus genotype for unique individuals. The PCID (1st column) is the sample ID. The Population_ID (2nd column) denotes the population assignment. Columns 3-32 represent the individual's genotype at each of the 15 microsatellite loci, with columns 3-4 representing both alleles for the first locus, columns 5-6 representing both alleles for the second locus, etc. Values of -99 indicate missing genotypes at a given locus. Sex (33rd column) represents the sex of the individual, with 'F' denoting female, 'M' denoting male, and '-99' denoting unknown. Collection_Year (34th column) denotes the year the sample was collected.

Life_Stages.csv - This file contains the life-stage assignment (calf, adult, or unknown) for each unique individual. Cluster_ID (1st column) represents the individual's ID. Capture_Year (2nd column) denotes the capture year. Age_Class (3rd column) denotes which life-stage the individual was assigned to in the provided capture year. Sex (4th column) denotes the sex of the individual. This file represents a subset of the data previously utilized by Flasko et al. 2017 and McFarlane et al. 2018.

Allele_Frequency.txt, ExcludedMaternity.txt, ExcludedPaternity.txt, Female_Genotype.txt, Male_Genotype.txt, Marker_Type_Error_Rate.txt, Offspring_Genotype.txt - These text files are the COLONY input files of the same name used to run COLONY for the caribou case study.

COLONY_Output.Maternity - This file is the maternity assignment file output by COLONY for the caribou case study. The 1st column represents the offspring's ID. The 2nd column represents the most likely mother's ID. The 3rd column denotes the probability that the most likely mother is the true mother of the given offspring. Columns 4 and 5 are the ID of the 2nd most likely mother and the probability that the 2nd most likely mother is the true mother of the given offspring (if applicable).

Code/Software

Caribou_CKMR_Sim_1000_Updated.R - This R script performs the close-kin mark-recapture simulation as implemented in the associated manuscript. This script is specifically for performing the simulation with a reproductive female abundance of 1000, although can also be used to perform the simulation for other population sizes by changing a few lines of code.

CKMR_Case_Study.R - This script is for using the close-kin mark-recapture abundance estimation framework to estimate female caribou abundance for a small boreal caribou population as implemented in the associated manuscript. Specifically, this script performs abundance estimation for the year 2006, but abundance for other years can be estimated by changing a single line of the code.