Changes in version 0.13.0

  New features
    -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
    
    Bug fixes
    -fixed a bug in editGenome when making multiple edits
    -adding merging of centromere vector in cChr

Changes in version 0.12.2
  
  New features
    -GxE traits now default to random sampling of p-values
  
  Bug fixes
    -fixed a bug in restrSegSites

Changes in version 0.12.1

  Bug fixes
    -fixed a bug in selection of segSites

Changes in version 0.12.0
  
  New features
    -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
  
  Bug fixes
    -fixed subset by id for populations
    -fixed major bug in newMapPop

Changes in version 0.11.1
  
  New features
    -switched to a circular design for the balance option in randCross and randCross2
    -added reduceGenome and doubleGenome for changing plody 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 
    
  Bug fixes
    -fixed broken SimParam_addStructuredSnpChip
    -removed broken pullMultipleSnpGeno and pullMultipleSnpHaplo
    -fixed broken writePlink

Changes in version 0.11.0
  
  New features
    -$MAJOR CHANGE$ 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
    
  Bug fixes
    -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

Changes in version 0.10.0
  
  New features
    -added traits with epistasis
    -Max number of threads automatically detected
    -added RRBLUP_D2
    -added version tracking to SimParam
    -removed trackHaploPop (superceded by pullIbdHaplo)
    -added fastRRBLUP
  
  Bug fixes
    -fixed faulty double crossover logic
    -fixed broken writePlink
    -fixed broken pullIbdHaplo
    -mergePops no longer assumes diploidy

Changes in version 0.9.0

  New features
    -added support for autopolyploids
    -added RRBLUP_GCA2
    -randCross2 can now "balance" crossing when not using gender
  
  Bug fixes
    -fixed recombination tracking bug in createDH2
    -removed bug in setEBV with append=TRUE

Changes in version 0.8.2

  Bug fixes
    -fixed ambiguous overloading in optimize.cpp

Changes in version 0.8.1

  Bug fixes
    -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

Changes in version 0.8.0

  New features
    -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
    
  Bug fixes
    -fixes for male selection in selectOP

Changes in version 0.7.1
  
  Bug fixes
    -add fixEff to setPhenoGCA

Changes in version 0.7.0

  New features
    -added default runMacs option to return all segSites
    -added ability to specify seperate male and female genetic maps
    -pullGeno and pullHaplo functions can now specifiy chromosomes
    -added RRBLUP2 for special GS cases
    -improved speed by replacing Rcpp random number generators
    -changed available MaCS species
    -$MAJOR CHANGE$ GS functions now use populations directly
    -added pullIbdHaplo
    -added writePlink
    
  Bug fixes
    -fixed population subsetting 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

Changes in version 0.6.1

  New features
    -selectFam now handles half-sib families
    -selectWithinFam now handles half-sib families
    
  Bug fixes
    -Removed restriction on varE=NULL in setPhenoGCA

Changes in version 0.6.0

  New features
    -Added NEWS file
    -Added selectOP to model selection in open pollinating plants
    -Added runMacs2 as a wrapper for runMacs
    
  Bug fixes
    -Fixed error when using H2 in SimParam_setVarE
    