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A package to perfrom individual-based simulations of genome evolution with ancestry.
Thijs Janzen gave a presentation demonstrating GenomeAdmixR (then named isoSIM) at the R User Group at the University of Groningen, Groningen, The Netherlands. You can watch his presentation here (audio starts after 1 min)
More information can be found in the accompanying paper : https://doi.org/10.1111/2041-210X.13612
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 1.00 -
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 underlying code tracking frequencies
Version 0.58 - Removed many old functions, and improved usability
for many existing functions
Version 0.58 - Renamed to
GenomeAdmixR
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