Description Usage Arguments Examples
View source: R/loadFineStructure.R
Read fineSTRUCTURE Output
1 2 | loadFineStructure(chunkfile, treefile, mcmcfile, meancoincidencefile = NULL,
mappopchunkfile = NULL)
|
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 |
1 2 3 4 5 6 7 8 | # 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
|
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