version 1.3.2, bugfix patch

gaynorr · Nov 2, 2022 · ecfbc87 · ecfbc87
1 parent d46f67f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.3.1.9990
-Date: 2022-9-27
+Version: 1.3.2
+Date: 2022-11-2
 Authors@R: c(person("Chris", "Gaynor", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0558-6656")),
   person("Gregor", "Gorjanc", role = "ctb", 

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,15 @@
-# AlphaSimR 1.3.1.9990
+# 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

diff --git a/R/Class-Pop.R b/R/Class-Pop.R
@@ -746,6 +746,11 @@ resetPop = function(pop,simParam=NULL){
     simParam = get("SP",envir=.GlobalEnv)
   }
   pop@nTraits = simParam$nTraits
+
+  # Extract names to add back at the end
+  traitNames = colnames(pop@gv)
+
+  # Create empty slots for traits
   pop@pheno = matrix(NA_real_,
                      nrow=pop@nInd,
                      ncol=simParam$nTraits)
@@ -756,6 +761,8 @@ resetPop = function(pop,simParam=NULL){
   pop@gv = matrix(NA_real_,nrow=pop@nInd,
                   ncol=simParam$nTraits)
   pop@fixEff = rep(1L,pop@nInd)
+
+  # Calculate genetic values
   if(simParam$nTraits>=1){
     for(i in 1:simParam$nTraits){
       tmp = getGv(simParam$traits[[i]],pop,simParam$nThreads)
@@ -765,6 +772,10 @@ resetPop = function(pop,simParam=NULL){
       }
     }
   }
+
+  # Add back trait names
+  colnames(pop@pheno) = colnames(pop@gv) = traitNames
+
   return(pop)
 }
 

diff --git a/R/misc.R b/R/misc.R
@@ -1,3 +1,9 @@
+# Converts a matrix to integer type
+# Intended for genotype matrices of raw type
+convToImat = function(X){
+  return(matrix(as.integer(X), nrow=nrow(X) ,ncol=ncol(X)))
+}
+
 #' @rdname isFemale
 #' @title Test if individuals of a population are female or male
 #'

diff --git a/R/pullGeno.R b/R/pullGeno.R
@@ -1,7 +1,3 @@
-convToImat = function(X){
-  return(matrix(as.integer(X), nrow=nrow(X) ,ncol=ncol(X)))
-}
-
 selectLoci = function(chr, inLociPerChr, inLociLoc){
   if(is.null(chr)){
     return(list(lociPerChr=inLociPerChr,