Description Usage Arguments Value Examples
View source: R/RunHybridCoal.R
This function returns vector.GeneTreeProbabilities: a vector of gene tree probabilities for the species model (sum ~1.0)
1 2 | RunHybridCoal(string.PathHybridCoal, handle.SpeciesTree,
string.PathParentDir, string.SpeciesTree.ModelName)
|
string.PathHybridCoal |
Path to HYBRID-COAL executable |
handle.SpeciesTree |
Species tree |
string.PathParentDir |
Path to a parent directory that will be used for subdirectories |
string.SpeciesTree.ModelName |
String giving the name of the species model |
vector.GeneTreeProbabilities: vector containing a set of gene tree probabilities for the species tree model
1 2 3 4 5 6 7 8 | string.SpeciesTree.1a <- "(((A:1,B:1):1,C:2):1,D:3);"
handle.SpeciesTree.1a <- read.tree(text = string.SpeciesTree.1a)
RunHybridCoal(string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal',
handle.SpeciesTree = handle.SpeciesTree.1a,
string.PathParentDir = '~/Desktop/EXAMPLE/SmallTree/',
string.SpeciesTree.ModelName = "Model1a")
|
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