# Estimate Kinship and FST under Arbitrary Population Structure

## Documentation for package ‘popkin’ version 1.3.17

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

popkin-package | A package for estimating kinship and FST under arbitrary population structure
avg_kinship_subpops | Calculate a kinship matrix between subpopulations by averaging individual data
fst | Calculate FST from a population-level kinship matrix or vector of inbreeding coefficients
inbr | Extract inbreeding coefficients from a kinship matrix
inbr_diag | Replace kinship diagonal with inbreeding coefficients
mean_kinship | Calculate the weighted mean kinship
n_eff | Calculates the effective sample size of the data
plot_admix | Make a structure/admixture plot
plot_phylo | Plot a 'phylo' tree object
plot_popkin | Visualize one or more kinship matrices and other related objects
popkin | Estimate kinship from a genotype matrix and subpopulation assignments
popkin_A | Compute popkin's 'A' and 'M' matrices from genotypes
popkin_af | Estimate coancestry from an allele frequency matrix and subpopulation assignments
popkin_A_min_subpops | Estimate the minimum expected value of a matrix 'A' using subpopulations
pwfst | Estimate the individual-level pairwise FST matrix
rescale_popkin | Rescale kinship matrix to set a given kinship value to zero.
validate_kinship | Validate a kinship matrix
weights_subpops | Get weights for individuals that balance subpopulations
_PACKAGE | A package for estimating kinship and FST under arbitrary population structure