loadFineStructure: Read fineSTRUCTURE Output

In sa-lee/starmie: Population Structure Model Inference and Visualisation

Description

Read fineSTRUCTURE Output

Usage

loadFineStructure(chunkfile, treefile, mcmcfile, meancoincidencefile = NULL,
  mappopchunkfile = NULL)

Arguments

chunkfile	a string containing a chunk counts file produce by fineStructure
treefile	a string containing a tree file produce by fineStructure
mcmcfile	a string containing a mcmc file produce by fineStructure
meancoincidencefile	(default=NULL) a string containing a pairwise coincidence produce by fineStructure
mappopchunkfile	(default=NULL) a string containing a population level chunk counts file produce by fineStructure

Examples

# read in example fineSTRUCTURE output
chunkfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.chunkcounts.out", package = "starmie")
treefile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.tree.xml", package = "starmie")
mcmcfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.mcmc.xml", package = "starmie")
meancoincidencefile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.meancoincidence.csv", package = "starmie")
mappopchunkfile <- system.file("extdata/fine_structure_files", "EastAsiaSimple.EMlinked.mapstate.csv", package = "starmie")
fineData <- loadFineStructure(chunkfile, treefile, mcmcfile, meancoincidencefile, mappopchunkfile)
fineData

sa-lee/starmie documentation built on May 28, 2019, 11 a.m.