sumStatsBranchLength: Compute branch lengths summary statistics

In ilajaait/deephylo: Infer Parameters from Phylogenies with Deep-Learning

Compute branch lengths summary statistics

Description

Compute the 25 summary statistics related to branch lengths listed below. A branch is external if linked to a tip, other the branch is internal. The branches are sorted in 3 parts regarding the time of the child.

Variable	Description
height	phylogeny height
mean.all	mean of all branch lengths
median.all	median of all branch lengths
var.all	variance of all branch lengths
mean.ext	mean of external branch lengths
median.ext	median of external branch lengths
var.ext	variance of external branch lengths
mean.int1	mean of internal branch lengths of part 1
median.int1	median of internal branch lengths of part 1
var.int1	variance of internal branch lengths of part 1
mean.int2	mean of internal branch lengths of part 2
median.int2	median of internal branch lengths of part 2
var.int2	variance of internal branch lengths of part 2
mean.int3	mean of internal branch lengths of part 3
median.int3	median of internal branch lengths of part 3
var.int3	variance of internal branch lengths of part 3
mean.intext1	mean.int1 / mean.ext
median.int1	median.int1 / median.ext
var.int1	var.int1 / var.ext
mean.intext2	mean.int2 / mean.ext
median.int2	median.int2 / median.ext
var.int2	var.int2 / var.ext
mean.intext3	mean.int3 / mean.ext
median.int3	median.int3 / median.ext
var.int3	var.int3 / var.ext

Usage

sumStatsBranchLength(phylo, df.edges)

Arguments

phylo	phylogeny (ape format)
df.edges	dataframe

Value

list

• $stat.all: statistic computed on all branch lengths (stat is either mean, median or var)

• $stat.ext: statistic computed on external branch lengths only

• $stat.inti: statistic computed on internal branch lengths only belonging to part i (i is either 1,2 or 3)

• $stat.intext1: $stat.inti / $stat.ext

See Also

Saulnier et al., 2014, PLOS

ilajaait/deephylo documentation built on April 10, 2022, 11:03 a.m.