Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. The simulation assumes Wright-Fisher dynamics, e.g. random mating and non-overlapping generations. In the simulation, instead of specific alleles, local ancestry is tracked, thus assuming that local molecular data can always be uniquely traced back to one of the founding individuals (populations). The package provides functionality to perform such simulations, but also to perform post-hoc statistical analyses and to visualize the obtained results.
Version 2.1.7 - Improve documentation Version 2.1.6 - check classes with inherits Version 2.1.5 - Removed debugging output Version 2.1.4 - Only output when verbose = TRUE Version 2.1.3 - Changed DOI link in description Version 2.1.2 - Improved testing Version 2.1.1 - Removed GNU make dependency Version 2.1 - Removed error in calculate_allele_frequency Version 2.0.1 - Moved migration outside the modules Version 2.0 - Added ancestry_module and sequence_module to distinguish between implementations of the model Version 1.2 - Added example sequencing data Version 1.2 - Added the option to load sequence data for admixing Version 1.1 - Fixed a minor bug with plot_joyplot_frequencies Version 1.1 - Improved tests Version 1.1 - Improved recombination code (again) Version 1.0 - Release associated with bioRxiv submission, to be found here: https://doi.org/10.1101/2020.10.19.343491 Version 0.66 - Improved recombination code, about twice as fast Version 0.65 - Added testing and added logo Version 0.64 - Reduced cyclomatic complexity Version 0.63 - Updated random number generation Version 0.62 - Updated to Roxygen Version 0.61 - Added plot_over_time Version 0.60 - Added admixture with migration Version 0.59 - Updated frequency code under the hood Version 0.58 - Renamed to GenomeAdmixR Version 0.58 - Collapsed and improved many functions Version 0.57 - Added function to generate admixed individuals Version 0.56 - Added starting frequencies to 'simulate_admixture' Version 0.55 - Extended 'calculate_marker_frequency' to handle a vector of locations Version 0.55 - Increased accuracy of choosing a random position for recombination, this should prevent the rare bug fixed in version 0.54 Version 0.54 - Fixed a MAJOR bug regarding recombination: in rare cases, a crossover position could be picked on an existing junction, due to the limited number of digits in uniform() Version 0.54 - Improved plot_difference_frequencies to handle modified input Version 0.53 - Added multiplicative_selection Version 0.52 - Added plot_difference_frequencies Version 0.51 - Added tajima's d calculation Version 0.50 - Added simulated_admixture until Version 0.49 - Added 'simulate' to cpp Version 0.48 - Added a general 'simulate' function Version 0.47 - Changed the effect of migration Version 0.46 - Added joyplot & increase_ancestor Version 0.45 - Removed create_two_populations Version 0.44 - Added tracking regions Version 0.43 - Fixed bugs in select_population Version 0.42 - Added initial and final frequency tables Version 0.41 - Added multiple marker support Version 0.40 - Collapsed selection functions Version 0.39 - Added support for non-additive selection Version 0.38 - Added track frequencies Version 0.37 - Removed selection on regions Version 0.36 - Added progress_bar option Version 0.35 - Added calculate_marker_frequency Version 0.34 - Added selection_markers Version 0.33 - Fixed bugs in selection Version 0.32 - Moved Fish.h code to Fish.cpp Version 0.31 - Changed random number generator to R based Version 0.30 - Added Recombination = 1 code Version 0.29 - Changed internal junction representation: removed .left Version 0.28 - Reverted to Agner Fog Random number generation Version 0.27 - Speed up return types Version 0.26 - Added class verification code Version 0.25 - Squashed plotting bug Version 0.24 - Removed Output.cpp Version 0.23 - Removed number_of_founders from calc_allele_spectrum Version 0.22 - Added save and load functions Version 0.21 - Changed random-seed management Version 0.20 - Removed superfluous code Version 0.19 - Removed number_of_founders from Fst and LD code Version 0.18 - Start of tracking changes
Janzen, T., Diaz, F. (2020) Individual-based simulations of genome evolution with ancestry: the GenomeAdmixR R package. bioRxiv 2020.10.19.343491; doi: https://doi.org/10.1101/2020.10.19.343491