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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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.