Merge pull request #116 from gaynorr/devel

Committing version 1.4.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.3.4
-Date: 2022-12-8
+Version: 1.4.2
+Date: 2023-3-27
 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", 
@@ -13,7 +13,9 @@ Authors@R: c(person("Chris", "Gaynor", email = "[email protected]",
   comment = c(ORCID = "0000-0001-5151-3648")),
   person("David", "Wilson", role = "ctb"),
   person("Thiago","Oliveira", role = "ctb",
-  comment = c(ORCID = "0000-0002-4555-2584")))
+  comment = c(ORCID = "0000-0002-4555-2584")),
+  person("Audrey", "Martin", role = "ctb",
+  comment = c(ORCID = "0000-0003-2235-0098")))
 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 
@@ -35,7 +37,7 @@ Depends: R (>= 4.0.0), methods, R6
 Imports: Rcpp (>= 0.12.7), Rdpack
 RdMacros: Rdpack
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Suggests: knitr, rmarkdown, testthat
 VignetteBuilder: knitr
 NeedsCompilation: true

NEWS.md

@@ -1,3 +1,19 @@
+# AlphaSimR 1.4.2
+
+* updated MaCS citation to https site
+
+# AlphaSimR 1.4.1
+
+* Changed citation to use `bibentry` instead of `citEntry`
+
+# AlphaSimR 1.4.0
+
+*fixed a bug in IBD tracking
+
+*add `setFounderHap` to SimParam for applying custom haplotypes to founders
+
+*added `addSnpChipByName` to SimParam for defining SNP chips by marker names
+
 # AlphaSimR 1.3.4
 
 *changed C++ using `sprintf` to use `snprintf`

R/Class-SimParam.R

@@ -315,6 +315,18 @@ SimParam = R6Class(
       }
       invisible(self)
     },
+
+    #' @description 
+    #' Allows for the manual setting of founder haplotypes. This functionality 
+    #' is not fully documented, because it is still experimental.
+    #' 
+    #' @param hapMap a list of founder haplotypes
+    setFounderHap = function(hapMap){
+      private$.hap = hapMap
+      private$.hasHap = rep(TRUE, length(hapMap))
+      private$.isFounder = rep(FALSE, length(hapMap))
+      invisible(self)
+    },
 
     #' @description
     #' Randomly assigns eligible SNPs to a SNP chip
@@ -347,6 +359,64 @@ SimParam = R6Class(
       self$snpChips[[self$nSnpChips + 1L]] = snpChip
       invisible(self)
     },
+
+    #' @description
+    #' Assigns SNPs to a SNP chip by supplying marker names. This function does 
+    #' check against excluded SNPs and will not add the SNPs to the list of 
+    #' excluded QTL for the purpose of avoiding overlap between SNPs and QTL. 
+    #' Excluding these SNPs from being used as QTL can be accomplished using 
+    #' the excludeQtl argument in SimParam's restrSegSites function.
+    #'
+    #' @param markers a vector of names for the markers
+    #' @param name optional name for chip
+    #'
+    #' @examples
+    #' #Create founder haplotypes
+    #' founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
+    #'
+    #' #Set simulation parameters
+    #' SP = SimParam$new(founderPop)
+    #' SP$addSnpChipByName(c("1_1","1_3"))
+    addSnpChipByName = function(markers, name=NULL){
+      genMap = private$.femaleMap
+
+      # Check that the markers are present on the map
+      genMapMarkerNames = unlist(lapply(genMap, names))
+      stopifnot(all(markers%in%genMapMarkerNames))
+
+      # Create lociPerChr and lociLoc
+      lociPerChr = integer(length(genMap))
+      lociLoc = vector("list", length(genMap))
+
+      # Loop through chromosomes
+      for(i in 1:length(genMap)){
+
+        # Initialize lociLoc
+        lociLoc[[i]] = integer()
+
+        # Find matches if they exist
+        take = match(names(genMap[[i]]), markers)
+        lociPerChr[i] = length(na.omit(take))
+        if(lociPerChr[i]>0L){
+          lociLoc[[i]] = which(!is.na(take))
+        }
+      }
+      lociLoc = unlist(lociLoc)
+
+      snpChip = new("LociMap",
+                    nLoci=sum(lociPerChr),
+                    lociPerChr=lociPerChr,
+                    lociLoc=lociLoc)
+
+      if(is.null(name)){
+        snpChip@name = paste0("Chip",self$nSnpChips + 1L)
+      }else{
+        snpChip@name = name
+      }
+
+      self$snpChips[[self$nSnpChips + 1L]] = snpChip
+      invisible(self)
+    },
 
     #' @description
     #' Randomly selects the number of snps in structure and then

R/RcppExports.R

@@ -264,14 +264,14 @@ getHybridGv <- function(trait, females, femaleParents, males, maleParents, nThre
     .Call(`_AlphaSimR_getHybridGv`, trait, females, femaleParents, males, maleParents, nThreads)
 }
 
-getFounderIbd <- function(founder, nChr) {
-    .Call(`_AlphaSimR_getFounderIbd`, founder, nChr)
-}
-
 getNonFounderIbd <- function(recHist, mother, father) {
     .Call(`_AlphaSimR_getNonFounderIbd`, recHist, mother, father)
 }
 
+getFounderIbd <- function(founder, nChr) {
+    .Call(`_AlphaSimR_getFounderIbd`, founder, nChr)
+}
+
 createIbdMat <- function(ibd, chr, nLoci, ploidy, nThreads) {
     .Call(`_AlphaSimR_createIbdMat`, ibd, chr, nLoci, ploidy, nThreads)
 }

inst/CITATION

@@ -1,16 +1,11 @@
-citHeader("To cite AlphaSimR in publications use:
-
-Gaynor, R. Chris, Gregor Gorjanc, and John M. Hickey. 2021. AlphaSimR: an R package for breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.")
-
-citEntry(
-  entry    = "Article",
+bibentry(
+  bibtype    = "Article",
   title    = "AlphaSimR: an R package for breeding program simulations",
   author   = "R Chris Gaynor, Gregor Gorjanc, John M Hickey",
   journal  = "G3 Gene|Genomes|Genetics",
   year     = "2021",
   volume   = "11",
   number   = "jkaa07",
   issue    = "2",
-  url      = "https://doi.org/10.1093/g3journal/jkaa017",
-  textVersion = ""
+  url      = "https://doi.org/10.1093/g3journal/jkaa017"
 )

inst/REFERENCES.bib

@@ -7,7 +7,7 @@ @article{MaCS
    volume = {19},
    pages = {136-142},
    year = {2009},
-   URL ={http://genome.cshlp.org/content/19/1/136}
+   URL ={https://genome.cshlp.org/content/19/1/136}
 }
 
 @article{AlphaSim,

src/RcppExports.cpp

@@ -563,18 +563,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// getFounderIbd
-arma::field<    arma::field<      arma::field<        arma::Mat<int> > > > getFounderIbd(const arma::field<arma::ivec>& founder, arma::uword nChr);
-RcppExport SEXP _AlphaSimR_getFounderIbd(SEXP founderSEXP, SEXP nChrSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const arma::field<arma::ivec>& >::type founder(founderSEXP);
-    Rcpp::traits::input_parameter< arma::uword >::type nChr(nChrSEXP);
-    rcpp_result_gen = Rcpp::wrap(getFounderIbd(founder, nChr));
-    return rcpp_result_gen;
-END_RCPP
-}
 // getNonFounderIbd
 arma::field<    arma::field<      arma::Mat<int> > > getNonFounderIbd(const arma::field<arma::field<arma::Mat<int> > >& recHist, const arma::field<arma::field<arma::Mat<int> > >& mother, const arma::field<arma::field<arma::Mat<int> > >& father);
 RcppExport SEXP _AlphaSimR_getNonFounderIbd(SEXP recHistSEXP, SEXP motherSEXP, SEXP fatherSEXP) {
@@ -588,6 +576,18 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// getFounderIbd
+arma::field<    arma::field<      arma::field<        arma::Mat<int> > > > getFounderIbd(const arma::field<arma::ivec>& founder, arma::uword nChr);
+RcppExport SEXP _AlphaSimR_getFounderIbd(SEXP founderSEXP, SEXP nChrSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const arma::field<arma::ivec>& >::type founder(founderSEXP);
+    Rcpp::traits::input_parameter< arma::uword >::type nChr(nChrSEXP);
+    rcpp_result_gen = Rcpp::wrap(getFounderIbd(founder, nChr));
+    return rcpp_result_gen;
+END_RCPP
+}
 // createIbdMat
 arma::Mat<int> createIbdMat(arma::field<arma::field<arma::field<arma::Mat<int> > > >& ibd, arma::uvec chr, arma::uvec nLoci, arma::uword ploidy, arma::uword nThreads);
 RcppExport SEXP _AlphaSimR_createIbdMat(SEXP ibdSEXP, SEXP chrSEXP, SEXP nLociSEXP, SEXP ploidySEXP, SEXP nThreadsSEXP) {
@@ -839,8 +839,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"_AlphaSimR_calcChrFreq", (DL_FUNC) &_AlphaSimR_calcChrFreq, 1},
     {"_AlphaSimR_getGv", (DL_FUNC) &_AlphaSimR_getGv, 3},
     {"_AlphaSimR_getHybridGv", (DL_FUNC) &_AlphaSimR_getHybridGv, 6},
-    {"_AlphaSimR_getFounderIbd", (DL_FUNC) &_AlphaSimR_getFounderIbd, 2},
     {"_AlphaSimR_getNonFounderIbd", (DL_FUNC) &_AlphaSimR_getNonFounderIbd, 3},
+    {"_AlphaSimR_getFounderIbd", (DL_FUNC) &_AlphaSimR_getFounderIbd, 2},
     {"_AlphaSimR_createIbdMat", (DL_FUNC) &_AlphaSimR_createIbdMat, 5},
     {"_AlphaSimR_cross", (DL_FUNC) &_AlphaSimR_cross, 15},
     {"_AlphaSimR_createDH2", (DL_FUNC) &_AlphaSimR_createDH2, 7},