preparing to release 1.3.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.2.2.9990
-Date: 2022-8-23
+Version: 1.3.0
+Date: 2022-8-24
 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", 
@@ -32,7 +32,8 @@ URL: https://github.com/gaynorr/AlphaSimR,
     https://www.edx.org/course/breeding-programme-modelling-with-alphasimr?utm_source=breeding_alphasimr&utm_medium=partner-marketing&utm_campaign=edinburghx
 Encoding: UTF-8
 Depends: R (>= 4.0.0), methods, R6
-Imports: Rcpp (>= 0.12.7)
+Imports: Rcpp (>= 0.12.7), Rdpack
+RdMacros: Rdpack
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
 RoxygenNote: 7.2.1
 Suggests: knitr, rmarkdown, testthat

NAMESPACE

@@ -132,6 +132,7 @@ exportClasses(TraitAEG)
 exportClasses(TraitAG)
 import(Rcpp)
 importFrom(R6,R6Class)
+importFrom(Rdpack,reprompt)
 importFrom(methods,.hasSlot)
 importFrom(methods,classLabel)
 importFrom(methods,is)

NEWS.md

@@ -1,19 +1,27 @@
-# AlphaSimR 1.2.2.9990
+# 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
 
-*add `addSegSite` for manually adding segregating sites to a MapPop class
+*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
@@ -48,7 +56,7 @@
 
 # AlphaSimR 1.1.1
 
-*removed use of PI variable in C++ code which is compiler specific
+*removed use of PI variable in C++ code due to it being compiler specific
 
 # AlphaSimR 1.1.0
 
@@ -90,7 +98,7 @@
 
 *changed to a Gamma Sprinkling model for crossovers, default is still a Gamma model
 
-*change default interfernce parameter (v) to 2.6 to be consistent with the Kosambi mapping function (was 1, consistent with the Haldane mapping function)
+*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
 

R/AlphaSimR.R

@@ -7,6 +7,7 @@
 #' @importFrom stats model.matrix rbinom runif cov2cor
 #' @importFrom utils combn read.table write.table packageDescription
 #' @importFrom R6 R6Class
+#' @importFrom Rdpack reprompt
 
 #' @description
 #' The successor to the 'AlphaSim' software for breeding program 

R/Class-Pop.R

@@ -375,8 +375,6 @@ isNamedMapPop = function(x) {
 #' @slot gxe list containing GxE slopes for GxE traits
 #' @slot fixEff a fixed effect relating to the phenotype.
 #' Used by genomic selection models but otherwise ignored.
-#' @slot reps the number of replications used to measure the
-#' phenotype. Used by genomic selection models, but otherwise ignored.
 #' @slot misc a list whose elements correspond to individuals in the
 #' population. This list is normally empty and exists solely as an
 #' open slot available for uses to store extra information about
@@ -395,7 +393,6 @@ setClass("Pop",
                  ebv="matrix",
                  gxe="list",
                  fixEff="integer",
-                 reps="numeric",
                  misc="list"),
          contains="RawPop")
 
@@ -455,9 +452,6 @@ setValidity("Pop",function(object){
   if(object@nInd!=length(object@fixEff)){
     errors = c(errors,"nInd!=length(fixEff)")
   }
-  if(object@nInd!=length(object@reps)){
-    errors = c(errors,"nInd!=length(reps)")
-  }
   if(object@nInd!=length(object@misc)){
     errors = c(errors,"nInd!=length(misc)")
   }
@@ -490,7 +484,6 @@ setMethod("[",
             x@mother = x@mother[i]
             x@father = x@father[i]
             x@fixEff = x@fixEff[i]
-            x@reps = x@reps[i]
             x@misc = x@misc[i]
             x@gv = x@gv[i,,drop=FALSE]
             x@pheno = x@pheno[i,,drop=FALSE]
@@ -692,7 +685,6 @@ newPop = function(rawPop,simParam=NULL,...){
                mother=mother,
                father=father,
                fixEff=rep(1L,rawPop@nInd),
-               reps=rep(1,rawPop@nInd),
                nTraits=simParam$nTraits,
                gv=gv,
                gxe=gxe,
@@ -764,7 +756,6 @@ resetPop = function(pop,simParam=NULL){
   pop@gv = matrix(NA_real_,nrow=pop@nInd,
                   ncol=simParam$nTraits)
   pop@fixEff = rep(1L,pop@nInd)
-  pop@reps = rep(1,pop@nInd)
   if(simParam$nTraits>=1){
     for(i in 1:simParam$nTraits){
       tmp = getGv(simParam$traits[[i]],pop,simParam$nThreads)
@@ -870,7 +861,6 @@ newEmptyPop = function(ploidy=2L, simParam=NULL){
                mother = character(),
                father = character(),
                fixEff = integer(),
-               reps = integer(),
                nTraits = simParam$nTraits,
                gv = traitMat,
                gxe = vector("list", simParam$nTraits),