*fixed bug in mergePops and [ (subset) methods - they were failing for populations that had a misc slot with a matrix - we now check if a misc slot element is a matrix and rbind them for mergePops and subset rows for [ (assuming the first dimension represents individuals)
*exported meanEBV and added varEBV to complement meanP/varP and meanG/varG
*Changed all parameters of the CATTLE demographic model to exactly match Macleod et al. (2013) - specifically reducing the mutation rate from 2.5e-8 (from human literature) to 1.2e-8 (used in Macleod et al., 2013) and recombination rate from 1e-8 (generic) to 9.26e-9 (used in Macleod et al., 2013). These changes will reduce number of segregating sites to ~240K per chromosome for 100 samples and will run faster.
*changed misc slot in Pop class from a list organised as ind x nodes to to a list organised as nodes x ind (this simplified code and increased speed)
*removed setMisc and getMisc because the new misc slot structure makes it easy to set and get misc components with base R code
*added length method for Pop class that returns number of individuals (like nInd)
*added length method for MultiPop class that returns number of populations
*fixed bug in quadrivalent pairing resulting in distribution of double reductions not respecting the centromere
*fixed bug in SimParam$restrSegSites with excluding sites at end of chromosome
*fix SimParam examples for CRAN
*deleted bad example code for setMisc
*changed examples to use a single thread for CRAN testing this change is not shown in the documentation
*renamed MegaPop to MultiPop
*fixed bug in writePlink to correctly export map positions in cM
*fixed bug in writeRecords due to removed reps slot in pops
*added altAddTraitAD for specifying traits with dominance effects using dominance variance and inbreeding depression
*add miscPop slot to class Pop
*updated MaCS citation to https site
*Changed citation to use bibentry instead of citEntry
*fixed a bug in IBD tracking
*add setFounderHap to SimParam for applying custom haplotypes to founders
*added addSnpChipByName to SimParam for defining SNP chips by marker names
*changed C++ using sprintf to use snprintf
*fixed bug in calculation of genic variance
*fixed importHaplo not passing ploidy to newMapPop
*fixed bug with correlated error variances
*fixed column name bug with multiple traits in setEBV
*fixed CTD caused by runMacs when too many segSites are requested
*fixed missing names in GV when using resetPop
*fixed bug in importTrait
*popVar now deals with matrices having 1 row
*updated link to Gaynor, 2017
*added ability to exclude loci by name in SimParam$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
*added getPed to quick extract a population's pedigree
*added getGenMap to pull a genetic map in data.frame format
*fixed bugs relating to importData functions
*fixed writePlink errors and no longer requires equal length chromosomes
*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
*added missing #ifdef _OPENMP to OCS.cpp
*removed use of PI variable in C++ code due to it being compiler specific
*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
*fixed errors in implementation of Gamma Sprinkling model
*fixed formatting error in genetic maps created by runMacs that broke genotype extraction functions
*added h2 and H2 to setPhenoGCA
*pullGeno and pullHaplo functions now report marker names from the genetic map
*removed lazyData field in DESCRIPTION
*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
*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
*GxE traits now default to random sampling of p-values
*fixed a bug in restrSegSites
*fixed a bug in selection of segSites
*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
*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
*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
*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
*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
*fixed ambiguous overloading in optimize.cpp
*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
*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
*add fixEff to setPhenoGCA
*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
*selectFam now handles half-sib families
*selectWithinFam now handles half-sib families
*Removed restriction on varE=NULL in setPhenoGCA
*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