Merge pull request #62 from gaynorr/devel

Devel

.Rbuildignore

@@ -8,3 +8,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^revdep$

.gitignore

@@ -2,9 +2,12 @@
 .Rhistory
 .RData
 .Ruserdata
+config.log
+config.status
 src/*.o
 src/*.so
 src/*.dll
 Notes.txt
 Meta
 .Rproj.user
+alphasimr.Rproj

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.1.2
-Date: 2022-2-17
+Version: 1.2
+Date: 2022-5-15
 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", 
@@ -11,7 +11,9 @@ Authors@R: c(person("Chris", "Gaynor", email = "[email protected]",
   comment = c(ORCID = "0000-0001-5675-3974")),
   person("Daniel", "Money", role = "ctb", 
   comment = c(ORCID = "0000-0001-5151-3648")),
-  person("David", "Wilson", role = "ctb"))
+  person("David", "Wilson", role = "ctb"),
+  person("Thiago","Oliveira", role = "ctb",
+  comment = c(ORCID = "0000-0002-4555-2584")))
 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 
@@ -27,7 +29,7 @@ Description: The successor to the 'AlphaSim' software for breeding program
 License: MIT + file LICENSE
 URL: https://github.com/gaynorr/AlphaSimR
 Encoding: UTF-8
-Depends: R (>= 3.3.0), methods, R6
+Depends: R (>= 4.0.0), methods, R6
 Imports: Rcpp (>= 0.12.7)
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
 RoxygenNote: 7.1.2

NAMESPACE

@@ -26,11 +26,17 @@ export(genicVarA)
 export(genicVarAA)
 export(genicVarD)
 export(genicVarG)
+export(getMisc)
 export(getNumThreads)
 export(getQtlMap)
 export(getSnpMap)
 export(gv)
 export(hybridCross)
+export(importGenMap)
+export(importHaplo)
+export(importInbredGeno)
+export(isFemale)
+export(isMale)
 export(makeCross)
 export(makeCross2)
 export(makeDH)
@@ -47,6 +53,8 @@ export(pedigreeCross)
 export(pheno)
 export(popVar)
 export(pullIbdHaplo)
+export(pullMarkerGeno)
+export(pullMarkerHaplo)
 export(pullQtlGeno)
 export(pullQtlHaplo)
 export(pullSegSiteGeno)
@@ -70,6 +78,7 @@ export(selectOP)
 export(selectWithinFam)
 export(self)
 export(setEBV)
+export(setMisc)
 export(setPheno)
 export(setPhenoGCA)
 export(setPhenoProgTest)
@@ -83,6 +92,7 @@ export(solveRRBLUP_EM)
 export(solveRRBLUP_EM2)
 export(solveRRBLUP_EM3)
 export(solveUVM)
+export(transMat)
 export(usefulness)
 export(varA)
 export(varAA)
@@ -119,9 +129,11 @@ importFrom(methods,show)
 importFrom(methods,validObject)
 importFrom(stats,aggregate)
 importFrom(stats,coef)
+importFrom(stats,cov2cor)
 importFrom(stats,dnorm)
 importFrom(stats,lm)
 importFrom(stats,model.matrix)
+importFrom(stats,na.omit)
 importFrom(stats,pnorm)
 importFrom(stats,qgamma)
 importFrom(stats,qnorm)
@@ -130,6 +142,7 @@ importFrom(stats,rnorm)
 importFrom(stats,runif)
 importFrom(stats,var)
 importFrom(utils,combn)
+importFrom(utils,packageDescription)
 importFrom(utils,read.table)
 importFrom(utils,write.table)
 useDynLib(AlphaSimR, .registration = TRUE)

NEWS

@@ -1,3 +1,17 @@
+Changes in version 1.2.0
+
+  New features
+    -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
+
+  Bug fixes
+    -reduceGenome, mergeGenome and doubleGenome should really now work with pedigree and recombination tracking
+
+  Known issues
+    -pedigreeCross fails without an appropriate warning for some incomplete pedigrees
+
 Changes in version 1.1.2
 
   Bug fixes

R/AlphaSimR.R

@@ -3,9 +3,9 @@
 #' @importFrom methods new validObject is .hasSlot 
 #' @importFrom methods show classLabel
 #' @importFrom stats aggregate rnorm qnorm var
-#' @importFrom stats coef dnorm lm pnorm qgamma
-#' @importFrom stats model.matrix rbinom runif
-#' @importFrom utils combn read.table write.table
+#' @importFrom stats coef dnorm lm pnorm qgamma na.omit
+#' @importFrom stats model.matrix rbinom runif cov2cor
+#' @importFrom utils combn read.table write.table packageDescription
 #' @importFrom R6 R6Class
 
 #' @description
@@ -22,7 +22,7 @@
 #' for fast simulation of biallelic sequences according to a population 
 #' demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
 #' 
-#' Please see the introductionary vignette for instructions for using this package. 
+#' Please see the introductory vignette for instructions for using this package. 
 #' The vignette can be viewed using the following command: 
 #' \code{vignette("intro",package="AlphaSimR")}
 #' @keywords internal

R/Class-HybridPop.R

@@ -93,7 +93,6 @@ setMethod("[",
                 }
               }
             }
-            validObject(x)
             return(x)
           }
 )
@@ -118,11 +117,11 @@ setMethod("c",
                 }
               }
             }
-            validObject(x)
             return(x)
           }
 )
 
+# Test if object is of a HybridPop class
 isHybridPop = function(x) {
   ret = is(x, class2 = "HybridPop")
   return(ret)

R/Class-LociMap.R

@@ -9,12 +9,15 @@
 #' @slot nLoci total number of loci
 #' @slot lociPerChr number of loci per chromosome
 #' @slot lociLoc physical position of loci
+#' @slot name optional name for LociMap object
 #'
 #' @export
 setClass("LociMap",
          slots=c(nLoci="integer",
                  lociPerChr="integer",
-                 lociLoc="integer"))
+                 lociLoc="integer",
+                 name="character"),
+         prototype=list(name=NA_character_))
 
 setValidity("LociMap",function(object){
   errors = character()
@@ -31,6 +34,7 @@ setValidity("LociMap",function(object){
   }
 })
 
+# Test if object is of a LociMap class
 isLociMap = function(x) {
   ret = is(x, class2 = "LociMap")
   return(ret)
@@ -63,6 +67,7 @@ setValidity("TraitA",function(object){
   }
 })
 
+# Test if object is of a TraitA class
 isTraitA = function(x) {
   ret = is(x, class2 = "TraitA")
   return(ret)
@@ -94,6 +99,7 @@ setValidity("TraitA2",function(object){
   }
 })
 
+# Test if object is of a TraitA2 class
 isTraitA2 = function(x) {
   ret = is(x, class2 = "TraitA2")
   return(ret)
@@ -127,6 +133,7 @@ setValidity("TraitAE",function(object){
   }
 })
 
+# Test if object is of a TraitAE class
 isTraitAE = function(x) {
   ret = is(x, class2 = "TraitAE")
   return(ret)
@@ -157,6 +164,7 @@ setValidity("TraitAD",function(object){
   }
 })
 
+# Test if object is of a TraitAD class
 isTraitAD = function(x) {
   ret = is(x, class2 = "TraitAD")
   return(ret)
@@ -187,6 +195,7 @@ setValidity("TraitA2D",function(object){
   }
 })
 
+# Test if object is of a TraitA2D class
 isTraitA2D = function(x) {
   ret = is(x, class2 = "TraitA2D")
   return(ret)
@@ -220,6 +229,7 @@ setValidity("TraitADE",function(object){
   }
 })
 
+# Test if object is of a TraitADE class
 isTraitADE = function(x) {
   ret = is(x, class2 = "TraitADE")
   return(ret)
@@ -254,6 +264,7 @@ setValidity("TraitAG",function(object){
   }
 })
 
+# Test if object is of a TraitAG class
 isTraitAG = function(x) {
   ret = is(x, class2 = "TraitAG")
   return(ret)
@@ -288,6 +299,7 @@ setValidity("TraitAEG",function(object){
   }
 })
 
+# Test if object is of a TraitAEG class
 isTraitAEG = function(x) {
   ret = is(x, class2 = "TraitAEG")
   return(ret)
@@ -322,6 +334,7 @@ setValidity("TraitADG",function(object){
   }
 })
 
+# Test if object is of a TraitADG class
 isTraitADG = function(x) {
   ret = is(x, class2 = "TraitADG")
   return(ret)
@@ -356,6 +369,7 @@ setValidity("TraitADEG",function(object){
   }
 })
 
+# Test if object is of a TraitADEG class
 isTraitADEG = function(x) {
   ret = is(x, class2 = "TraitADEG")
   return(ret)