ts read and write (double cross over breakpoints included)

.github/workflows/R-CMD-check.yaml

@@ -43,7 +43,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: github::LynxJinyangii/RcppTskit/RcppTskit@add-multiple-functions-on-pr-131, any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/document.yaml

@@ -29,7 +29,7 @@ jobs:
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::roxygen2
+          extra-packages: github::LynxJinyangii/RcppTskit/RcppTskit@add-multiple-functions-on-pr-131, any::roxygen2
           needs: roxygen2
 
       - name: Document

.github/workflows/pkgdown.yaml

@@ -30,7 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: github::LynxJinyangii/RcppTskit/RcppTskit@add-multiple-functions-on-pr-131, any::pkgdown, local::.
           needs: website
 
       - name: Build site

.github/workflows/test-coverage.yaml

@@ -36,7 +36,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, any::xml2
+          extra-packages: github::LynxJinyangii/RcppTskit/RcppTskit@add-multiple-functions-on-pr-131, any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage

.gitignore

@@ -10,6 +10,7 @@
 .Rhistory
 .Rproj.user/
 .Ruserdata
+.Rproj.user.bak/
 .httr-oauth
 /*.Rcheck/
 /.*tar.gz
@@ -30,3 +31,38 @@ src/Makevars
 src/Makevars.win
 vignettes/*.html
 vignettes/*.pdf
+.idea/
+src/.idea/
+.Rlib/
+*tar.gz
+__pycache__/
+testData/out_phase1_useMacsMut_FALSE/*.trees
+testData/out_msprime_from_macs/*.trees
+dev/testData/out_phase1_useMacsMut_FALSE/*.trees
+dev/testData/out_msprime_from_macs/*.trees
+dev/testData/AlphaSimR_extended_TS_*.trees
+dev/testData/inbred_test.trees
+dev/testData/forward_*.trees
+dev/testData/msprime_bridge_*.trees
+dev/testData/msprime_direct_*.trees
+dev/testData/runMacTS_bridge_*.trees
+dev/testData/runMacTS_direct_*.trees
+dev/testData/runMacTS_founder_*.trees
+dev/testData/runMacsTS_bridge_*.trees
+dev/testData/runMacsTS_direct_*.trees
+dev/testData/runMacsTS_founder_*.trees
+dev/testData/standard_forward_recorder_*.trees
+dev/testData/standard_*_forward_recorder_*.trees
+dev/testData/standard_msprime_*_input_forward_recorder_*.trees
+dev/testData/standard_msprime_vcf_addTsMut_forward_recorder_*.trees
+!dev/testData/*.vcf
+!dev/testData/AlphaSimR_extended_chr*.trees
+!dev/testData/MaCSTS*.trees
+!dev/testData/msprime_chr*.trees
+dev/testData/*_pairs.json
+dev/testData/hotspots*.txt
+dev/testData/*_hotspots_for_window_counts.txt
+dev/testData/out_phase1_useMacsMut_FALSE/*.debug.txt
+dev/testData/out_phase1_useMacsMut_FALSE/*.demography.png
+dev/*.html
+dev/tmp_tree.*

DESCRIPTION

@@ -43,8 +43,7 @@ Depends: R (>= 4.0.0)
 Imports: Rcpp (>= 0.12.7), Rdpack, methods, R6, RcppTskit (>= 0.3.0)
 RdMacros: Rdpack
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH, dqrng (>= 0.4.1), RcppTskit
-RoxygenNote: 7.3.3
 Suggests: knitr, rmarkdown, testthat
 VignetteBuilder: knitr
 NeedsCompilation: true
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -14,6 +14,7 @@ export(aa)
 export(addSegSite)
 export(asCategorical)
 export(asLogNormal)
+export(asMapPop)
 export(asPoisson)
 export(attrition)
 export(bv)
@@ -41,6 +42,7 @@ export(hybridCross)
 export(importGenMap)
 export(importHaplo)
 export(importInbredGeno)
+export(importVCF)
 export(isFemale)
 export(isHybridPop)
 export(isMale)
@@ -89,6 +91,7 @@ export(rtsk_table_collection_summary2)
 export(rtsk_treeseq_get_num_individuals2)
 export(runMacs)
 export(runMacs2)
+export(runMacsTS)
 export(sampleHaplo)
 export(selIndex)
 export(selInt)
@@ -104,6 +107,8 @@ export(setMarkerHaplo)
 export(setPheno)
 export(setPhenoGCA)
 export(setPhenoProgTest)
+export(simAnc)
+export(simMut)
 export(smithHazel)
 export(solveMKM)
 export(solveMVM)
@@ -114,6 +119,9 @@ export(solveRRBLUP_EM)
 export(solveRRBLUP_EM2)
 export(solveRRBLUP_EM3)
 export(solveUVM)
+export(tsForwardFinalizeFromSimParam)
+export(tsForwardHasRecorder)
+export(tsForwardWriteTreesFromSimParam)
 export(unnameMultiPop)
 export(usefulness)
 export(varA)
@@ -146,31 +154,37 @@ import(Rcpp)
 import(RcppTskit)
 importFrom(R6,R6Class)
 importFrom(Rdpack,reprompt)
-importFrom(methods,.hasSlot)
-importFrom(methods,classLabel)
-importFrom(methods,is)
-importFrom(methods,new)
-importFrom(methods,show)
-importFrom(methods,slot)
-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)
-importFrom(stats,rbinom)
-importFrom(stats,rnorm)
-importFrom(stats,rpois)
-importFrom(stats,runif)
-importFrom(stats,setNames)
-importFrom(stats,var)
-importFrom(utils,combn)
-importFrom(utils,packageDescription)
-importFrom(utils,read.table)
-importFrom(utils,write.table)
+importFrom(methods,
+  .hasSlot,
+  classLabel,
+  is,
+  new,
+  show,
+  slot,
+  validObject
+)
+importFrom(stats,
+  aggregate,
+  coef,
+  cov2cor,
+  dnorm,
+  lm,
+  model.matrix,
+  na.omit,
+  pnorm,
+  qgamma,
+  qnorm,
+  rbinom,
+  rnorm,
+  rpois,
+  runif,
+  setNames,
+  var
+)
+importFrom(utils,
+  combn,
+  packageDescription,
+  read.table,
+  write.table
+)
 useDynLib(AlphaSimR, .registration = TRUE)

R/Class-Pop.R

@@ -686,7 +686,7 @@ newPop = function(rawPop,ploidy=NULL,simParam=NULL,nThreads=NULL,...){
 .newPop = function(rawPop, id=NULL, mother=NULL, father=NULL,
                    iMother=NULL, iFather=NULL, isDH=NULL,
                    femaleParentPop=NULL, maleParentPop=NULL,
-                   hist=NULL, simParam=NULL, nThreads=NULL,...){
+                   hist=NULL, histGen=NULL, simParam=NULL, nThreads=NULL,...){
   if(is.null(simParam)){
     simParam = get("SP",envir=.GlobalEnv)
   }
@@ -813,7 +813,7 @@ newPop = function(rawPop,ploidy=NULL,simParam=NULL,nThreads=NULL,...){
 
   if(simParam$isTrackPed){
     if(simParam$isTrackRec){
-      simParam$addToRec(lastId,id,iMother,iFather,isDH,hist,output@ploidy)
+      simParam$addToRec(lastId,id,iMother,iFather,isDH,hist,histGen,output@ploidy) #Jinyang modified
     }else{
       simParam$addToPed(lastId,id,iMother,iFather,isDH)
     }
@@ -823,6 +823,14 @@ newPop = function(rawPop,ploidy=NULL,simParam=NULL,nThreads=NULL,...){
 
   output = simParam$finalizePop(output, simParam=simParam, ...)
 
+  ts_forward_attrs <- c("tsForwardSource", "tsForwardPosMeta")
+  for (nm in ts_forward_attrs) {
+    val <- attr(rawPop, nm, exact = TRUE)
+    if (!is.null(val)) {
+      attr(output, nm) <- val
+    }
+  }
+
   return(output)
 }
 
@@ -1534,4 +1542,4 @@ unnameMultiPop = function(x, level = Inf) {
   }
   validObject(mp)
   return(mp)
-}
+}