GenomeAdmixR-package: Simulate Admixture of Genomes
In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes
GenomeAdmixR-package R Documentation
Simulate Admixture of Genomes
Description
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
Author(s)
Thijs Janzen
Maintainer: (thijsjanzen@gmail.com)
References
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
thijsjanzen/GenomeAdmixR documentation built on Feb. 16, 2024, 7:27 p.m.
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| GenomeAdmixR-package | R Documentation |
Simulate Admixture of Genomes
Description
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
Author(s)
Thijs Janzen Maintainer: (thijsjanzen@gmail.com)
References
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
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