GenomeAdmixR-package    Simulate Admixture of Genomes
ancestry_module         Creates a module to start simulations tracking
                        local ancestry
calculate_allele_frequencies
                        Calculate allele frequencies
calculate_average_ld    Calculates the ld between two alleles
calculate_dist_junctions
                        collect the full distribution of junctions in
                        the population
calculate_fst           Calculate FST
calculate_heterozygosity
                        Calculate heterozygosity
calculate_ld            Calculate linkage disequilibrium statistics
                        This function calculates two matrices, once
                        containing all pairwise linkage disequilibrium
                        (ld) values, and one matrix containing all
                        pairwise r statistics
calculate_marker_frequency
                        Calculate allele frequencies at a specific
                        marker location
combine_input_data      combine sequence data that was previously read
                        from file into a population
create_artificial_genomeadmixr_data
                        function to generate artificial
                        genomeadmixr_data
create_iso_female       function to simulate creation of an isofemale
                        line
dgrp2.3R.5k.data        A subset of sequencing data from the Drosophila
                        Genetics Reference Panel
iso_female_ancestry     Create isofemale
iso_female_sequence     Create isofemale
load_population         Load a population from file
migration_settings      Function to manage settings associated with
                        migration
plink_to_genomeadmixr_data
                        function to convert plink style (ped/map) data
                        to genome_admixr_data
plot.individual         plot the genome of an individual
plot_chromosome         plots a chromosome
plot_difference_frequencies
                        Plot the change in frequency between the start
                        and end of a simulation
plot_dist_junctions     plot the distribution of junctions
plot_frequencies        Plot the frequencies of all ancestors along the
                        genome.
plot_joyplot_frequencies
                        make a joy plot of the distribution of allele
                        frequencies within a region
plot_over_time          Plot the frequencies of all ancestors over time
plot_start_end          Plot both the starting frequencies and the
                        final frequencies in one plot
print.genomeadmixr_data
                        print an individual to the console
print.individual        print an individual to the console
print.population        print a population object
read_input_data         read sequence data from file to be used in
                        simulation
save_population         Save a population to file
sequence_module         create sequence module
simulate_admixture      Individual based simulation of the breakdown of
                        contiguous ancestry blocks.
simulate_ancestry       Individual based simulation of the breakdown of
                        contiguous ancestry blocks.
simulate_ancestry_migration
                        Individual based simulation of the breakdown of
                        contiguous ancestry blocks in two populations
                        linked by migration
simulate_sequence       Individual based simulation of the breakdown of
                        contiguous ancestry blocks.
simulate_sequence_migration
                        Individual based simulation of the breakdown of
                        contiguous ancestry blocks in two populations
                        linked by migration
simulation_data_to_genomeadmixr_data
                        function to convert ped/map data to
                        genome_admixr_data
vcfR_to_genomeadmixr_data
                        function to convert a vcfR object to
                        genome_admixr_data
write_as_plink          function to write simulation output as PLINK
                        style data
