createAstralPlaneCF: createAstralPlaneCF

In chutter/AstralPlane: R Package For Preparing, Running, Analyzing and Plotting for the Species Tree Program ASTRAL-III

createAstralPlaneCF

Description

Function for reading data into the astralPlane format

Usage

createAstralPlaneCF(cf.file.name = NULL, outgroups = NULL, tip.length = 1)

Arguments

cf.file.name	prefix file name of the file for concordance factors
outgroups	a vector of outgroups to root the tree
tip.length	arbitrary value for the terminal tip lengths, Astral does not compute this
astral.tree	file path to your tree

Value

an S4 Object of class astralPlane. The object is slotted and contains: 1. Sample names, 2. phylogenetic tree rooted, 3. node.data table of ASTRAL-III node data, 4. edge.data table of ASTRAL-III branch data. All these make ASTRAL-III output readable and easy to use in other functions, or to plot using the astralProjection function.

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/AstralPlane documentation built on Aug. 29, 2024, 5:21 p.m.