[pull] master from gaynorr:master

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.6.1
-Date: 2024-11-01
+Version: 2.0.0
+Date: 2025-09-01
 Authors@R: c(person("Chris", "Gaynor", email = "gaynor.robert@hotmail.com",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0558-6656")),
   person("Gregor", "Gorjanc", role = "ctb", 
@@ -17,7 +17,9 @@ Authors@R: c(person("Chris", "Gaynor", email = "gaynor.robert@hotmail.com",
   person("Audrey", "Martin", role = "ctb",
   comment = c(ORCID = "0000-0003-2235-0098")),
   person("Philip", "Greenspoon", role = "ctb",
-  comment = c(ORCID = "0000-0001-6284-7248")))
+  comment = c(ORCID = "0000-0001-6284-7248")),
+  person("Ros", "Craddock", role = "ctb",
+  comment = c(ORCID = "0009-0004-1578-1580")))
 Description: The successor to the 'AlphaSim' software for breeding program 
   simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. 
   Used for stochastic simulations of breeding programs to the level of DNA 

NAMESPACE

@@ -12,6 +12,7 @@ export(RRBLUP_SCA2)
 export(SimParam)
 export(aa)
 export(addSegSite)
+export(asCategorical)
 export(attrition)
 export(bv)
 export(cChr)
@@ -102,7 +103,6 @@ export(solveRRBLUP_EM)
 export(solveRRBLUP_EM2)
 export(solveRRBLUP_EM3)
 export(solveUVM)
-export(transMat)
 export(usefulness)
 export(varA)
 export(varAA)

NEWS.md

@@ -1,3 +1,17 @@
+# AlphaSimR 2.0.0
+
+*added names to `SP$recHist`
+
+*added `asCategorical` to convert a normal (Gaussian) trait to an ordered categorical (threshold) trait
+
+*improved computational performance of simulations with multiple traits
+
+*added support for data.frames in SimParam genetic map switching functions
+
+*changed finalizePop function call in `.newPop` to pass simParam as an argument
+
+*updated version numbering to follow tidyverse format with a major version indicating backwards compatibility has been broken
+
 # AlphaSimR 1.6.1
 
 *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)

R/Class-Pop.R

@@ -615,7 +615,7 @@ newPop = function(rawPop,simParam=NULL,...){
   return(.newPop(rawPop=rawPop,simParam=simParam,...))
 }
 
-#' @title Create new population (internal)
+#' @title Create new population
 #'
 #' @description
 #' Creates a new \code{\link{Pop-class}} from an object of
@@ -636,6 +636,8 @@ newPop = function(rawPop,simParam=NULL,...){
 #' function in simParam
 #'
 #' @return Returns an object of \code{\link{Pop-class}}
+#' 
+#' @keywords internal
 .newPop = function(rawPop, id=NULL, mother=NULL, father=NULL,
                    iMother=NULL, iFather=NULL, isDH=NULL,
                    femaleParentPop=NULL, maleParentPop=NULL,
@@ -711,14 +713,19 @@ newPop = function(rawPop,simParam=NULL,...){
   pheno = gv
 
   if(simParam$nTraits>=1){
+    tmp = getGvIndex(rawPop, simParam$traits, simParam$activeQtl, 
+                     simParam$qtlIndex, simParam$nTraits, simParam$nThreads)
+
+    gv = tmp[[1]]
+    colnames(gv) = simParam$traitNames
+
+    gxeTmp = tmp[[2]]
+    dim(gxeTmp) = NULL # Account for matrix bug in RcppArmadillo
+
+    # Move over gxeTmp for traits with GxE
     for(i in seq_len(simParam$nTraits)){
-      tmp = getGv(simParam$traits[[i]], rawPop, simParam$nThreads)
-      gv[,i] = tmp[[1]]
-
-      colnames(gv)[i] = simParam$traits[[i]]@name
-
-      if(length(tmp)>1){
-        gxe[[i]] = tmp[[2]]
+      if(.hasSlot(simParam$traits[[i]], "gxeEff")){
+        gxe[[i]] = gxeTmp[[i]]
       }
     }
   }
@@ -750,7 +757,7 @@ newPop = function(rawPop,simParam=NULL,...){
                       simParam=simParam)
   }
 
-  output = simParam$finalizePop(output,...)
+  output = simParam$finalizePop(output, simParam=simParam, ...)
 
   if(simParam$isTrackPed){
     if(simParam$isTrackRec){