Package: GenomeAdmixR 2.1.13.2

GenomeAdmixR: Simulate Admixture of Genomes

Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.

Authors:Thijs Janzen [aut, cre], Fernando Diaz G. [ctb], Richèl J.C. Bilderbeek [ctb]

GenomeAdmixR_2.1.13.2.tar.gz
GenomeAdmixR_2.1.13.2.zip(r-4.7)GenomeAdmixR_2.1.13.2.zip(r-4.6)GenomeAdmixR_2.1.13.2.zip(r-4.5)
GenomeAdmixR_2.1.13.2.tgz(r-4.6-x86_64)GenomeAdmixR_2.1.13.2.tgz(r-4.6-arm64)GenomeAdmixR_2.1.13.2.tgz(r-4.5-x86_64)GenomeAdmixR_2.1.13.2.tgz(r-4.5-arm64)
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GenomeAdmixR_2.1.13.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GenomeAdmixR/json (API)

# Install 'GenomeAdmixR' in R:
install.packages('GenomeAdmixR', repos = c('https://thijsjanzen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thijsjanzen/genomeadmixr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • dgrp2.3R.5k.data - A subset of sequencing data from the Drosophila Genetics Reference Panel

On CRAN:

Conda:

cpp

5.95 score 5 stars 24 scripts 628 downloads 33 exports 79 dependencies

Last updated from:eb580131ff. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK209
linux-devel-x86_64OK200
source / vignettesOK299
linux-release-arm64OK211
linux-release-x86_64OK180
macos-release-arm64OK128
macos-release-x86_64OK320
macos-oldrel-arm64OK142
macos-oldrel-x86_64OK342
windows-develOK253
windows-releaseOK175
windows-oldrelOK212
wasm-releaseOK170

Exports:ancestry_modulecalculate_allele_frequenciescalculate_average_ldcalculate_dist_junctionscalculate_fstcalculate_heterozygositycalculate_ldcalculate_marker_frequencycombine_input_datacreate_artificial_genomeadmixr_datacreate_iso_femaledefault_params_dociso_female_ancestryiso_female_sequenceload_populationmigration_settingsplink_to_genomeadmixr_dataplot_chromosomeplot_difference_frequenciesplot_dist_junctionsplot_frequenciesplot_joyplot_frequenciesplot_over_timeplot_start_endread_input_datasave_populationsequence_modulesimulate_admixturesimulate_ancestry_migrationsimulate_sequence_migrationsimulation_data_to_genomeadmixr_datavcfR_to_genomeadmixr_datawrite_as_plink

Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercommonmarkcpp11digestdplyrfarverfastmapfontawesomefsgastongenericsggplot2ggridgesgluegtablegtoolshierfstathtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisememusemgcvmimenlmeotelpermutepillarpinfsc50pixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangS7sassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithrxtable

Demonstrate isofemales
Creation of isofemale lines
Rendered fromDemonstrate_isofemales.Rmdusingknitr::rmarkdown

Last update: 2026-05-13
Started: 2018-11-21

Demonstrate joyplot
Demonstration of how to use joyplots
Rendered fromJoyplots.Rmdusingknitr::rmarkdown

Last update: 2026-05-13
Started: 2018-11-21

Empirical data
Migration | Using simulation data as input | Mutation rate
Rendered fromEmpirical_data.Rmdusingknitr::rmarkdown

Last update: 2026-05-13
Started: 2021-01-28

Walkthrough
GenomeAdmixR | Simulating an iso-female line | Visualizing individuals | Multiple source populations | Statistics | FST | LD | Selection
Rendered fromWalkthrough.Rmdusingknitr::rmarkdown

Last update: 2026-05-13
Started: 2018-11-21

Visualization
Plot over time | Plot Frequencies | plot difference frequencies | plot_start_end | joyplots | Plotting individual chromosomes
Rendered fromVisualization.Rmdusingknitr::rmarkdown

Last update: 2026-05-12
Started: 2021-01-13

Readme and manuals

Help Manual

Help pageTopics
Simulate Admixture of GenomesGenomeAdmixR-package GenomeAdmixR
Creates a module to start simulations tracking local ancestryancestry_module
Calculate allele frequenciescalculate_allele_frequencies
Calculates the ld between two allelescalculate_average_ld
collect the full distribution of junctions in the populationcalculate_dist_junctions
Calculate FSTcalculate_fst
Calculate heterozygositycalculate_heterozygosity
Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statisticscalculate_ld
Calculate allele frequencies at a specific marker locationcalculate_marker_frequency
combine sequence data that was previously read from file into a populationcombine_input_data
function to generate artificial genomeadmixr_datacreate_artificial_genomeadmixr_data
function to simulate creation of an isofemale linecreate_iso_female
A subset of sequencing data from the Drosophila Genetics Reference Paneldgrp2.3R.5k.data
Create isofemaleiso_female_ancestry
Create isofemaleiso_female_sequence
Load a population from fileload_population
Function to manage settings associated with migrationmigration_settings
function to convert plink style (ped/map) data to genome_admixr_dataplink_to_genomeadmixr_data
plots a chromosomeplot_chromosome
Plot the change in frequency between the start and end of a simulationplot_difference_frequencies
plot the distribution of junctionsplot_dist_junctions
Plot the frequencies of all ancestors along the genome.plot_frequencies
make a joy plot of the distribution of allele frequencies within a regionplot_joyplot_frequencies
Plot the frequencies of all ancestors over timeplot_over_time
Plot both the starting frequencies and the final frequencies in one plotplot_start_end
plot the genome of an individualplot.individual
print an individual to the consoleprint.genomeadmixr_data
print an individual to the consoleprint.individual
print a population objectprint.population
read sequence data from file to be used in simulationread_input_data
Save a population to filesave_population
create sequence modulesequence_module
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_admixture
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_ancestry
Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migrationsimulate_ancestry_migration
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_sequence
Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migrationsimulate_sequence_migration
function to convert ped/map data to genome_admixr_datasimulation_data_to_genomeadmixr_data
function to convert a vcfR object to genome_admixr_datavcfR_to_genomeadmixr_data
function to write simulation output as PLINK style datawrite_as_plink