GenomeAdmixR2.1.7 package

Creates a module to start simulations tracking local ancestry

Calculate allele frequencies

Calculates the ld between two alleles

collect the full distribution of junctions in the population

Calculate FST

Calculate heterozygosity

Calculate linkage disequilibrium statistics This function calculates t...

Calculate allele frequencies at a specific marker location

combine sequence data that was previously read from file into a popula...

function to generate artificial genomeadmixr_data

function to simulate creation of an isofemale line

Simulate Admixture of Genomes

Create isofemale

Create isofemale

Load a population from file

Function to manage settings associated with migration

function to convert plink style (ped/map) data to genome_admixr_data

plot the genome of an individual

plots a chromosome

Plot the change in frequency between the start and end of a simulation

plot the distribution of junctions

Plot the frequencies of all ancestors along the genome.

make a joy plot of the distribution of allele frequencies within a reg...

Plot the frequencies of all ancestors over time

Plot both the starting frequencies and the final frequencies in one pl...

print an individual to the console

print an individual to the console

print a population object

read sequence data from file to be used in simulation

Save a population to file

create sequence module

Individual based simulation of the breakdown of contiguous ancestry bl...

Individual based simulation of the breakdown of contiguous ancestry bl...

Individual based simulation of the breakdown of contiguous ancestry bl...

Individual based simulation of the breakdown of contiguous ancestry bl...

Individual based simulation of the breakdown of contiguous ancestry bl...

function to convert ped/map data to genome_admixr_data

function to convert a vcfR object to genome_admixr_data

function to write simulation output as PLINK style data