# Simulate Admixture of Genomes

## Documentation for package ‘GenomeAdmixR’ version 2.1.1

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

## Help Pages

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
GenomeAdmixR | Simulate Admixture of Genomes
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