AlphaSimR 1.5.3

*fixed bug in SimParam$restrSegSites with excluding sites at end of chromosome

AlphaSimR 1.5.2

*fix SimParam examples for CRAN

AlphaSimR 1.5.1

*deleted bad example code for setMisc

*changed examples to use a single thread for CRAN testing this change is not shown in the documentation

AlphaSimR 1.5.0

*renamed MegaPop to MultiPop

*fixed bug in writePlink to correctly export map positions in cM

*fixed bug in writeRecords due to removed reps slot in pops

*added altAddTraitAD for specifying traits with dominance effects using dominance variance and inbreeding depression

*add miscPop slot to class Pop

AlphaSimR 1.4.2

*updated MaCS citation to https site

AlphaSimR 1.4.1

*Changed citation to use bibentry instead of citEntry

AlphaSimR 1.4.0

*fixed a bug in IBD tracking

*add setFounderHap to SimParam for applying custom haplotypes to founders

*added addSnpChipByName to SimParam for defining SNP chips by marker names

AlphaSimR 1.3.4

*changed C++ using sprintf to use snprintf

AlphaSimR 1.3.3

*fixed bug in calculation of genic variance

*fixed importHaplo not passing ploidy to newMapPop

*fixed bug with correlated error variances

AlphaSimR 1.3.2

*fixed column name bug with multiple traits in setEBV

*fixed CTD caused by runMacs when too many segSites are requested

*fixed missing names in GV when using resetPop

*fixed bug in importTrait

*popVar now deals with matrices having 1 row

AlphaSimR 1.3.1

*updated link to Gaynor, 2017

AlphaSimR 1.3.0

*added ability to exclude loci by name in SimParam$restrSegSites

*pullMarkerGeno and pullMarkerHaplo now work with a MapPop class

*added setMarkerHaplo to manually change genotypes in a Pop or MapPop

*added addSegSite for manually adding segregating sites to a MapPop class

*simParam$setCorE has been deprecated in favor of a corE argument in simParam$setVarE

*setPheno now takes corE as an argument

*setPheno now allows the user to set phenotypes for a subset of traits

*add newEmptyPop to create populations with zero individuals

*removed reps slot from populations and heterogeneous residual variance GS models

*added h2, H2, and corE to setPhenoGCA and setPhenoProgTest

*the “EUROPEAN” species history was removed from runMacs due to lengthy runtime

AlphaSimR 1.2.2

*added getPed to quick extract a population’s pedigree

*added getGenMap to pull a genetic map in data.frame format

AlphaSimR 1.2.1

*fixed bugs relating to importData functions

*fixed writePlink errors and no longer requires equal length chromosomes

AlphaSimR 1.2.0

*added importGenMap to format genetic maps for AlphaSimR

*added importInbredGeno and importHaplo to make it easier to create a simulation from external data

*added importSnpChip, importTrait to SimParam to make it easier to manually define traits

*added pullMarkerGeno and pullMarkerHaplo to make it easier to extract genotypes and haplotypes of specific loci without defining a trait or SNP chip

*reduceGenome, mergeGenome and doubleGenome should really now work with pedigree and recombination tracking

AlphaSimR 1.1.2

*added missing #ifdef _OPENMP to OCS.cpp

AlphaSimR 1.1.1

*removed use of PI variable in C++ code due to it being compiler specific

AlphaSimR 1.1.0

*added snpChip argument to pullIbdHaplo for backwards compatibility

*exposed internal mixed model solvers

*all selection functions now return a warning when there are not enough individuals

*fixed error in pullIbdHaplo when chr isn’t NULL

*fixed an error with assigning 1 QTL and/or SNP

*changed geno slot from matrix to list to support future RcppArmadillo changes

*doubleGenome and reduceGenome now work with IBD tracking

AlphaSimR 1.0.4

*fixed errors in implementation of Gamma Sprinkling model

AlphaSimR 1.0.3

*fixed formatting error in genetic maps created by runMacs that broke genotype extraction functions

AlphaSimR 1.0.2

*added h2 and H2 to setPhenoGCA

*pullGeno and pullHaplo functions now report marker names from the genetic map

AlphaSimR 1.0.1

*removed lazyData field in DESCRIPTION

AlphaSimR 1.0.0

*AlphaSimR manuscript has been published in G3 (citation added)

*changed to a Gamma Sprinkling model for crossovers, default is still a Gamma model

*change default interference parameter (v) to 2.6 to be consistent with the Kosambi mapping function (was 1, consistent with the Haldane mapping function)

*new internal id (iid) that allows user to freely change id slot in populations

*runMacs2 now adjusts Ne for autopolyploids

*parent populations are now passed to finalizePop

*check added that throws an error when use of discontinued “gender” argument is detected

*added experimental MegaPop-class

AlphaSimR 0.13.0

*references to gender have been changed to the more appropriate terms sex or sexes

*added misc slot to populations

*added finalizePop to SimParam

*added physical positions to getSnpMap and getQtlMap

*you can now use h2 and H2 to specify error variance in setPheno

*SimParam$setVarE now accepts a matrix for varE

*fixed a bug in editGenome when making multiple edits

*adding merging of centromere vector in cChr

AlphaSimR 0.12.2

*GxE traits now default to random sampling of p-values

*fixed a bug in restrSegSites

AlphaSimR 0.12.1

*fixed a bug in selection of segSites

AlphaSimR 0.12.0

*changed output of genParam to match Bulmer, 1976

*nProgeny added to makeCross and makeCross2

*all SimParam documentation is now in ?SimParam

*non-overlapping QTL and SNP is now the default

*new interface for restrSegSites in SimParam

*fixed subset by id for populations

*fixed major bug in newMapPop

AlphaSimR 0.11.1

*switched to a circular design for the balance option in randCross and randCross2

*added reduceGenome and doubleGenome for changing ploidy levels

*added minSnpFreq to SimParam_addSnpChip for any reference population

*the c function now merges individuals for MapPop objects (was chromosomes before)

*the cChr function new merges chromosomes for MapPop objects

*fixed broken SimParam_addStructuredSnpChip

*removed broken pullMultipleSnpGeno and pullMultipleSnpHaplo

*fixed broken writePlink

AlphaSimR 0.11.0

*rework of setEBV (breaks some scripts)

*genotype data now stored as bits (was bytes)

*implemented a gamma model for crossover interference

*added the mutate function to model random mutations

*added a vignette explaining the biological model for traits

*GS models now handle polyploids

*heterogenous error variance is now optional in GS models (default is homogeneous error)

*improved gene drop functionality of pedigreeCross

*added keepParents option to makeDH and self (indirectly extends selectFam and selectWithinFam)

*added RRBLUP_SCA2

*set methods for the “show” function when applied to populations

*fixed a bug returning the first individual when selecting 0

*fixed error in recombination track when using makeDH

*fixed error causing epistatic effects to mask GxE effects

*fixed an error with pullSegSiteGeno and pullSegSiteHaplo with variable number of sites per chromosome

AlphaSimR 0.10.0

*added traits with epistasis

*Max number of threads automatically detected

*added RRBLUP_D2

*added version tracking to SimParam

*removed trackHaploPop (super-ceded by pullIbdHaplo)

*added fastRRBLUP

*fixed faulty double crossover logic

*fixed broken writePlink

*fixed broken pullIbdHaplo

*mergePops no longer assumes diploidy

AlphaSimR 0.9.0

*added support for autopolyploids

*added RRBLUP_GCA2

*randCross2 can now “balance” crossing when not using gender

*fixed recombination tracking bug in createDH2

*removed bug in setEBV with append=TRUE

AlphaSimR 0.8.2

*fixed ambiguous overloading in optimize.cpp

AlphaSimR 0.8.1

*setPheno (not setPhenoGCA) passes the number of reps to populations

*fixed bug in editGenomeTopQtl

*fixed bug in RRBLUP_D

*fixed bug in resetPop

*fixed bug in SimParam_rescaleTraits

*removed unimplemented SimParam_restrSnpSites and SimParam_restrQtlSites

*add error message for no traits in calcGCA

AlphaSimR 0.8.0

*added GxE traits with zero environmental variance

*faster trait scaling

*faster calculation of genetic values

*dsyevr now called via arma_fortran

*added OpenMP support

*parallelized cross2

*parallelized runMacs

*parallelized calculation of genetic values

*variance calculations now account for inbreeding

*fixes for male selection in selectOP

AlphaSimR 0.7.1

*add fixEff to setPhenoGCA

AlphaSimR 0.7.0

*added default runMacs option to return all segSites

*added ability to specify separate male and female genetic maps

*pullGeno and pullHaplo functions can now specify chromosomes

*added RRBLUP2 for special GS cases

*improved speed by replacing Rcpp random number generators

*changed available MaCS species

*GS functions now use populations directly

*added pullIbdHaplo

*added writePlink

*fixed population sub-setting checks to prevent invalid selections

*fixed slow calcGCA

*fixed error in addTraitAG preventing multiple traits

*fixed bug with mergePops when merging ebv

*fixed bug in setVarE when using H2 and multiple traits

AlphaSimR 0.6.1

*selectFam now handles half-sib families

*selectWithinFam now handles half-sib families

*Removed restriction on varE=NULL in setPhenoGCA

AlphaSimR 0.6.0

*Added NEWS file

*Added selectOP to model selection in open pollinating plants

*Added runMacs2 as a wrapper for runMacs

*Fixed error when using H2 in SimParam_setVarE