isoSIM-package: This package simulates the generation of an isofemale line

In thijsjanzen/isoSIM: Simulate Linkage Disequilibrium Along Chromosomes in Isofemale Lines

Description

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

Details

This section should provide a more detailed overview of how to use the package, including the most important functions.

Author(s)

Thijs Janzen ([e-mail])

thijsjanzen/isoSIM documentation built on May 29, 2019, 10:39 a.m.