phrapl-example: A description for applying phrapl to a test dataset

In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description

A test dataset called TestData.rda can be found in the data directory included in the phrapl package. This dataset comprises 10 gene trees containing three populations ("A","B", and "C"), with 20 samples per population, and a single outgroup sample ("D"). Genealogies were simulated under a coalescent isolation only model where the true history is where populations A and B coalesce after 4Ne generations, population A-B coalesces with C after 10Ne generations and population A-B-C coalesces with D after 20Ne generations.

To access this dataset, simply load the file into R; e.g., data(TestData).

Five objects are included: 1. migrationArray, which lists specifications for six models to be analyzed (model number 1 corresponds to the correct model); 2. migrationArrayMap, which lists parameter indexes for each model included in migrationArray; 3. trees, which contains the 10 full gene trees in newick format; 4. assignFile, which gives assignments of samples to populations; 5. popAssignments, which gives a list of vectors describing how the dataset should be subsampled (e.g., list(c(3,3,3)) means that one subsampling procedure should be carried out, where 3 individuals are sampled from populations A, B, and C).

Subsampling (using PrepSubsampling) and weights calculation (using GetPermutationWeightsAcrossSubsamples) can first be carried out using assignFile popAssignments, and trees.

A phrapl GridSearch can be run using the output from these functions in addition to migrationArray and migrationArrayMap.

Examples

  data(TestData)
  ## Not run: 
  #Run PrepSubsampling on this dataset to get
  #10 subsample iterations per tree. Include
  #everything in the working directory
  observedTrees<-PrepSubsampling(assignmentsGlobal=assignFile,
    observedTrees<-trees,popAssignments=popAssignments,
    subsamplesPerGene=10)

  #To get the weights
  subsampleWeights.df<-GetPermutationWeightsAcrossSubsamples(
    popAssignments=popAssignments,observedTrees=observedTrees)

  #To get migrationArrayMap
  migrationArrayMap <- GenerateMigrationArrayMap(migrationArray)
  
  #To run a grid search
  result<-GridSearch(migrationArrayMap=migrationArrayMap,migrationArray=
    migrationArray,modelRange=1:6,popAssignments=popAssignments,
    observedTrees=observedTrees,subsampleWeights.df=subsampleWeights.df,
    subsamplesPerGene=10,totalPopVector=rep(20,10),nTrees=1e3,
    print.results=TRUE,return.all=TRUE)

  #To save the results to a file
  save(list=ls(), file="phraplOutput.rda")

  #To generate an output table
  totalData<-ConcatenateResults(rdaFiles="phraplOutput.rda",
  	outFile="AIC_table.txt")
    
## End(Not run)

bomeara/phrapl documentation built on Feb. 8, 2021, 6:45 p.m.