First v2.0 commit with @DaTa data.table slot

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: strataG
 Title: Summaries and Population Structure Analyses of Genetic Data
 Description: A toolkit for analyzing stratified population genetic data.
-Version: 1.0.7
+Version: 2.0.0
 License: GNU General Public License
 Authors@R: c(
   EA = person("Eric", "Archer", email = "eric.archer@noaa.gov", role = c("aut", "cre")),
@@ -12,21 +12,24 @@ Authors@R: c(
 URL: https://github.com/EricArcher/strataG
 BugReports: https://github.com/EricArcher/strataG/issues
 Depends:
-    R (>= 3.2.0),
-    apex,
-    adegenet
+    R (>= 3.2.0)
 Suggests:
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat
 Imports:
+    adegenet,
     ape,
+    apex,
+    data.table,
     copula,
     DT,
     ggplot2,
     graphics,
     grid,
     gridExtra,
     Hmisc,
+    Kmisc,
     methods,
     pegas,
     phangorn,
@@ -45,6 +48,7 @@ Collate:
     is.gtypes.R
     initialize.gtypes.R
     strataG-internal.R
+    as.array.gtypes.R
     as.matrix.gtypes.R
     as.data.frame.gtypes.R
     alleleFreqFormat.R
@@ -58,21 +62,17 @@ Collate:
     createConsensus.R
     dupGenotypes.R
     evanno.R
-    expectedNumAlleles.R
     fasta.R
     fastsimcoal.input.R
     fastsimcoal.R
     fixedDifferences.R
     fixedSites.R
     freq2GenData.R
-    fstToNm.R
     fusFs.R
     gelato.R
     genepop.R
     heterozygosity.R
-    Hstats.R
     hweTest.R
-    idRows.R
     iupacCode.R
     jackHWE.R
     labelHaplotypes.R
@@ -90,10 +90,11 @@ Collate:
     nucleotideDivergence.R
     nucleotideDiversity.R
     numAlleles.R
-    numGensEq.R
+    numGenotyped.R
     numMissing.R
     permuteStrata.R
     phase.R
+    popGenEqns.R
     popStructStat.R
     popStructTest.R
     privateAlleles.R
@@ -106,12 +107,6 @@ Collate:
     sharedLoci.R
     show.gtypes.R
     simGammaHaps.R
-    statChi2.R
-    statFis.R
-    statFst.R
-    statGst.R
-    statJostD.R
-    statPhist.R
     strataGUI.R
     strataSplit.R
     stratify.R
@@ -127,14 +122,13 @@ Collate:
     trimNs.R
     validIupacCodes.R
     variableSites.R
-    wrightFst.R
     write.gtypes.R
     write.nexus.snapp.R
     gtypes2genind.R
     gtypes2loci.R
+    gtypes2phyDat.R
     df2gtypes.R
     sequence2gtypes.R
-    gtypes2phyDat.R
 LazyData: true
 VignetteBuilder: knitr
 LinkingTo: Rcpp

NAMESPACE

@@ -47,7 +47,6 @@ export(gtypes2genind)
 export(gtypes2loci)
 export(gtypes2phyDat)
 export(hweTest)
-export(idRows)
 export(is.gtypes)
 export(isTi)
 export(isTv)
@@ -56,7 +55,6 @@ export(jackHWE)
 export(jackInfluential)
 export(labelHaplotypes)
 export(ldNe)
-export(loci)
 export(loci2gtypes)
 export(lowFreqSubs)
 export(mRatio)
@@ -70,6 +68,7 @@ export(neiDa)
 export(nucleotideDivergence)
 export(nucleotideDiversity)
 export(numAlleles)
+export(numGenotyped)
 export(numGensEq)
 export(numMissing)
 export(obsvdHet)
@@ -85,7 +84,6 @@ export(phaseWrite)
 export(phyDat2gtypes)
 export(popStructTest)
 export(privateAlleles)
-export(propSharedIds)
 export(propSharedLoci)
 export(propUniqueAlleles)
 export(qaqc)
@@ -139,12 +137,12 @@ exportMethods("description<-")
 exportMethods("schemes<-")
 exportMethods("strata<-")
 exportMethods(alleleNames)
+exportMethods(as.array)
 exportMethods(as.data.frame)
 exportMethods(as.matrix)
 exportMethods(description)
 exportMethods(indNames)
 exportMethods(locNames)
-exportMethods(loci)
 exportMethods(nInd)
 exportMethods(nLoc)
 exportMethods(nStrata)
@@ -158,8 +156,10 @@ exportMethods(summary)
 import(adegenet)
 import(ape)
 import(apex)
+import(data.table)
 importFrom(DT,datatable)
 importFrom(Hmisc,all.is.numeric)
+importFrom(Kmisc,readlines)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(Rcpp,sourceCpp)
 importFrom(copula,Stirling1)
@@ -230,7 +230,6 @@ importFrom(stats,reorder)
 importFrom(stats,sd)
 importFrom(stats,var)
 importFrom(swfscMisc,diversity)
-importFrom(swfscMisc,harmonic.mean)
 importFrom(swfscMisc,odds)
 importFrom(swfscMisc,pVal)
 importFrom(swfscMisc,zero.pad)

R/RcppExports.R

@@ -1,20 +1,16 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-indGenotype <- function(nInd, numAlleles, locus) {
-    .Call('strataG_indGenotype', PACKAGE = 'strataG', nInd, numAlleles, locus)
-}
-
-HoCalc <- function(nInd, loci, ploidy, strata, strataN) {
-    .Call('strataG_HoCalc', PACKAGE = 'strataG', nInd, loci, ploidy, strata, strataN)
+HoCalc <- function(nInd, locus, ploidy, strata, strataN) {
+    .Call('strataG_HoCalc', PACKAGE = 'strataG', nInd, locus, ploidy, strata, strataN)
 }
 
 HsCalc <- function(alleleFreq, ploidy, strataN, harmN, Ho) {
     .Call('strataG_HsCalc', PACKAGE = 'strataG', alleleFreq, ploidy, strataN, harmN, Ho)
 }
 
-Hstats_C <- function(loci, strata, ploidy) {
-    .Call('strataG_Hstats_C', PACKAGE = 'strataG', loci, strata, ploidy)
+Hstats_C <- function(loci, strata) {
+    .Call('strataG_Hstats_C', PACKAGE = 'strataG', loci, strata)
 }
 
 getMaxInt <- function(x) {
@@ -45,32 +41,32 @@ numOuterC <- function(x, y) {
     .Call('strataG_numOuterC', PACKAGE = 'strataG', x, y)
 }
 
-intVecToMat <- function(x, ncol) {
-    .Call('strataG_intVecToMat', PACKAGE = 'strataG', x, ncol)
+idStart <- function(id, ploidy) {
+    .Call('strataG_idStart', PACKAGE = 'strataG', id, ploidy)
 }
 
-numVecToMat <- function(x, ncol) {
-    .Call('strataG_numVecToMat', PACKAGE = 'strataG', x, ncol)
+idGenotype <- function(locus, id, ploidy) {
+    .Call('strataG_idGenotype', PACKAGE = 'strataG', locus, id, ploidy)
 }
 
-calcStrataN <- function(locus, strata) {
-    .Call('strataG_calcStrataN', PACKAGE = 'strataG', locus, strata)
+calcStrataN <- function(locus, strata, ploidy) {
+    .Call('strataG_calcStrataN', PACKAGE = 'strataG', locus, strata, ploidy)
 }
 
-statChi2_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statChi2_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statChi2_C <- function(loci, strataMat) {
+    .Call('strataG_statChi2_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-statFis_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statFis_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statFis_C <- function(loci, strataMat) {
+    .Call('strataG_statFis_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-alleleFreqCalc <- function(locVec, strata, ploidy) {
-    .Call('strataG_alleleFreqCalc', PACKAGE = 'strataG', locVec, strata, ploidy)
+alleleFreqCalc <- function(locVec, strataRep) {
+    .Call('strataG_alleleFreqCalc', PACKAGE = 'strataG', locVec, strataRep)
 }
 
-prHetCalc <- function(alleles, nvec, locusMat, strata, ploidy) {
-    .Call('strataG_prHetCalc', PACKAGE = 'strataG', alleles, nvec, locusMat, strata, ploidy)
+prHetCalc <- function(locus, nalleles, strata, nvec, ploidy) {
+    .Call('strataG_prHetCalc', PACKAGE = 'strataG', locus, nalleles, strata, nvec, ploidy)
 }
 
 varCompCalc <- function(nvec, alleleFreq, prHet, r, nbar, rnbar, nc) {
@@ -81,28 +77,28 @@ fstCalc <- function(loci, strata, ploidy) {
     .Call('strataG_fstCalc', PACKAGE = 'strataG', loci, strata, ploidy)
 }
 
-statFst_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statFst_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statFst_C <- function(loci, strataMat) {
+    .Call('strataG_statFst_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-statFstPrime_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statFstPrime_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statFstPrime_C <- function(loci, strataMat) {
+    .Call('strataG_statFstPrime_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-statGst_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statGst_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statGst_C <- function(loci, strataMat) {
+    .Call('strataG_statGst_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-statGstPrime_C <- function(loci, strataMat, ploidy, primeType) {
-    .Call('strataG_statGstPrime_C', PACKAGE = 'strataG', loci, strataMat, ploidy, primeType)
+statGstPrime_C <- function(loci, strataMat, primeType) {
+    .Call('strataG_statGstPrime_C', PACKAGE = 'strataG', loci, strataMat, primeType)
 }
 
-statGstDblPrime_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statGstDblPrime_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statGstDblPrime_C <- function(loci, strataMat) {
+    .Call('strataG_statGstDblPrime_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
-statJostD_C <- function(loci, strataMat, ploidy) {
-    .Call('strataG_statJostD_C', PACKAGE = 'strataG', loci, strataMat, ploidy)
+statJostD_C <- function(loci, strataMat) {
+    .Call('strataG_statJostD_C', PACKAGE = 'strataG', loci, strataMat)
 }
 
 ssWPCalc <- function(strataFreq, strataHapFreq, hapDist) {

R/alleleFreqFormat.R

@@ -38,7 +38,7 @@ alleleFreqFormat <- function(x, g) {
     # skip (leave as NA) if either id or locus can't be found
     if(!(id %in% indNames(g) | locus %in% locNames(g))) next
     # get genotype of this id at this locus
-    gt <- unlist(loci(g, id, locus))
+    gt <- as.array(g, id, locus)
     # if the genotype is NA skip and leave format as NA
     if(any(is.na(gt))) next
     # get frequency and round

R/alleleFreqs.R

@@ -22,28 +22,31 @@
 #' data(msats.g)
 #' 
 #' f <- alleleFreqs(msats.g)
-#' f$D11t # Frequencies for Locus D11t
+#' f$D11t # Frequencies and proportions for Locus D11t
 #' 
 #' f.pop <- alleleFreqs(msats.g, TRUE)
-#' f.pop$EV94[, , "Coastal"] # Frequencies for EV94 in the Coastal population
+#' f.pop$EV94[, "freq", "Coastal"] # Frequencies for EV94 in the Coastal population
 #' 
 #' @export
 
 alleleFreqs <- function(g, by.strata = FALSE) {
-  freqs <- vector("list", length = ncol(g@loci))
-  strata <- rep(g@strata, g@ploidy)
-  for(i in 1:length(freqs)) {
-    if(by.strata & nlevels(strata) != 1) {
-      f <- table(g@loci[, i], strata)
+  freqs <- vector("list", length = nLoc(g))
+  names(freqs) <- locNames(g)
+  if(by.strata & nStrata(g) > 1) {
+    for(i in locNames(g)) {
+      f <- table(g@data[[i]], g@data$strata)
       p <- prop.table(f, 2)
-      freqs[[i]] <- array(dim = list(nrow(f), 2, ncol(f)))
+      freqs[[i]] <- array(
+        dim = list(nrow(f), 2, ncol(f)),
+        dimnames = list(rownames(f), c("freq", "prop"), colnames(f))
+      )
       for(j in 1:ncol(f)) freqs[[i]][, , j] <- cbind(f[, j], p[, j])
-      dimnames(freqs[[i]]) <- list(rownames(f), c("freq", "prop"), colnames(f))
-    } else {
-      f <- table(g@loci[, i])
+    } 
+  } else {
+    for(i in locNames(g)) {
+      f <- table(g@data[[i]])
       freqs[[i]] <- cbind(freq = f, prop = f / sum(f))
     }
   }
-  names(freqs) <- colnames(g@loci)
   freqs
 }