# Analysing 'SNP' Data to Support Captive Breeding

## Documentation for package ‘dartR.captive’ version 1.2.2

- DESCRIPTION file.

## Help Pages

gl.assign.grm | Population assignment using grm
gl.assign.mahal | Calculate probabilities of assignment of an individual of unknown provenance to population based on Mahalanobis Distance
gl.assign.mahalanobis | Calculate probabilities of assignment of an individual of unknown provenance to population based on Mahalanobis Distance
gl.assign.on.genotype | Use genotype to identify populations as possible source populations for an individual of unknown provenance.
gl.assign.pa | Use private alleles to identify populations as possible source populations for an individual of unknown provenance.
gl.assign.pca | Eliminate from consideration putative source populations for a specified individual of unknown provenance using PCA
gl.diagnostics.relatedness | Run simulations and relatedness analyses on genlight objects
gl.filter.parent.offspring | Filters putative parent offspring within a population
gl.grm | Calculates an identity by descent matrix
gl.grm.network | Represents a similarity matrix as a network
gl.plot.network | Represents a distance or dissimilarity matrix as a network
gl.report.parent.offspring | Identifies putative parent offspring within a population
gl.run.colony | Run COLONY2
gl.run.EMIBD9 | Run program EMIBD9
gl.sim.relatedness | Simulate relatedness estimates.
gl2colony | Export a COLONY2 input file from a genlight object
utils.assignment | Population assignment probabilities
utils.assignment_2 | Population assignment probabilities
utils.assignment_3 | Population assignment probabilities
utils.assignment_4 | Population assignment probabilities