Pipeline.SpeciesTreeDistances.ScaleAllBranches: Pipeline.SpeciesTreeDistances.ScaleAllBranches: function to...

In radamsRHA/PSTDistanceR: Computing probabilistic distances between species tree models

Description

This function returns a matrix containing the 5 distance metics (3 probabilistic + Robinson-Foulds + BHV)

Usage

Pipeline.SpeciesTreeDistances.ScaleAllBranches(vector.ScaleFactor,
  string.PathParentDir, string.PathHybridCoal, handle.SpeciesTree.Model1,
  handle.SpeciesTree.Model2)

Arguments

vector.ScaleFactor	Vector to containing the values to scale the branches of the second species tree model
string.PathParentDir	Path to a parent directory that will be used for subdirectories
string.PathHybridCoal	Path to HYBRID-COAL executable
handle.SpeciesTree.Model1	Species Tree Model 1
handle.SpeciesTree.Model2	Species Tree Model 2

Value

XXX

Examples

library(phangorn)
library(PSTD)
library(distory)

string.SpeciesTree.1a <- "(((A:1,B:1):1,C:2):1,D:3);"
handle.SpeciesTree.1a <- read.tree(text = string.SpeciesTree.1a)

vector.Gamma <- seq(0.01, 10, 0.01)
handle.Figure1d <- Pipeline.SpeciesTreeDistances.ScaleAllBranches(vector.ScaleFactor = vector.Gamma, 
   string.PathParentDir = '~/Desktop/', 
   string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal', 
   handle.SpeciesTree.Model1 = handle.SpeciesTree.1a, 
   handle.SpeciesTree.Model2 = handle.SpeciesTree.1a)
   
plot(handle.Figure1d[,1], ylim = c(0, 0.75), col = "darkblue", type = "l", xaxt='n', yaxt="n", lty = 1)
axis(1,at=seq(from = 0, to = 1000, by = 50),labels=seq(from = 0, to = 10, by = 0.50))
axis(2,at=seq(from = 0, to = 0.75, by = 0.10),labels=seq(from = 0, to = 0.75, by = 0.10))
lines(handle.Figure1d[,2], col = "blue", lty = 2)
lines(handle.Figure1d[,3], col = "lightblue", lty = 4)
lines(handle.Figure1d[,5]*0.025, col = "red", lty = 3)

radamsRHA/PSTDistanceR documentation built on March 4, 2020, 11:03 a.m.