Added 64 bit word compiler flag

Working on writeRecords

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: AlphaSimR
 Type: Package
-Title: Breeding Program Simulation Tools
-Version: 0.1
+Title: Breeding Program Simulations
+Version: 0.1.1
 Author: Chris Gaynor
 Maintainer: Chris Gaynor <[email protected]>
 Description: This package contains classes and functions for simulating plant and animal breeding programs.
-License: GPL (>= 2)
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends: MASS
 Imports: Rcpp (>= 0.12.7), RcppArmadillo (>= 0.7.500.0.0), methods
 LinkingTo: Rcpp, RcppArmadillo
 RoxygenNote: 5.0.1
-Suggests: knitr, rmarkdown
+Suggests: knitr, rmarkdown, testthat
 VignetteBuilder: knitr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2017
+COPYRIGHT HOLDER: R Chris Gaynor

NAMESPACE

@@ -30,6 +30,7 @@ export(setPhenoGCA)
 export(varAD)
 export(varG)
 export(varP)
+export(writeRecords)
 exportClasses(HybridPop)
 exportClasses(LociMap)
 exportClasses(MapPop)

R/AlphaSimR.R

@@ -4,7 +4,7 @@
 #' @importFrom stats aggregate rnorm
 #' @importFrom utils combn
 
-#' @title AlphaSimR: A package for simulating breeding programs.
+#' @title AlphaSimR: Breeding Program Simulations
 #' 
 #' @description
 #' This package is currently under development and is not yet ready for release.

R/GS.R

@@ -0,0 +1,37 @@
+#' @title Write data records
+#' 
+#' @description
+#' Saves a population's phenotypic and marker data to a directory.
+#'
+#' @param pop an object of \code{\link{Pop-class}}
+#' @param dir directory for saving output
+#' @param snpChip which SNP chip genotype to save. If useQtl=TRUE, this 
+#' value will indicate which trait's QTL genotype to save.
+#' @param useQtl should QTL genotype be written instead of SNP chip 
+#' genotypes.
+#' @param simParam an object of \code{\link{SimParam-class}}
+#'
+#' @export
+writeRecords = function(pop,dir,snpChip,useQtl=FALSE,simParam=SIMPARAM){
+  stopifnot(dir.exists(dir))
+  if(useQtl){
+    nMarkers = simParam@traits[[snpChip]]@nLoci
+    markerType = paste0("QTL_",snpChip)
+  }else{
+    nMarkers = simParam@snpChips[[snpChip]]@nLoci
+    markerType = paste0("SNP_",snpChip)
+  }
+  #Check that the marker set isn't being changed
+  markerInfo = data.frame(markerType=markerType,
+                          nMarkers=nMarkers,
+                          stringsAsFactors=FALSE)
+  markerInfoPath = file.path(dir,"markerInfo.txt")
+  if(file.exists(markerInfoPath)){
+    tmp = read.table(markerInfoPath,stringsAsFactors=FALSE)
+    stopifnot(identical(tmp,markerInfo))
+  }else{
+    write.table(markerInfo,markerInfoPath)
+  }
+
+
+}

R/SavedData.R

@@ -0,0 +1,14 @@
+#' @title Example MapPop
+#' 
+#' @description An object of \code{\link{MapPop-class}} containing 
+#' two individuals with one chromosome with one Morgan length. Both 
+#' individuals are fully inbred and have 1001 segregating sites on 
+#' 1 chromosome. The first individual has all '1' alleles and the 
+#' second individual has all '0' alleles.
+#' 
+#' @docType data
+#' 
+#' @usage data(PopTwo)
+#' 
+#' @format An object of \code{\link{MapPop-class}}
+"PopTwo"

inst/doc/examples.R

@@ -1,5 +1,5 @@
 # AlphaSimR Examples
-# Works with version 0.1
+# Works with version 0.1.X
 
 # *Requires MaCS
 # Which can be taken from AlphaSim on the AlphaGenes website

src/Makevars

@@ -1 +1,2 @@
+CPPFLAGS = -DARMA_64BIT_WORD=1
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,2 +1,3 @@
 
+CPPFLAGS = -DARMA_64BIT_WORD=1
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(AlphaSimR)
+
+test_check("AlphaSimR")