pdist.p: Pairwise phylogenetic distance matrix from small tree

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

Pairwise phylogenetic distance matrix from small tree

Description

Calculates between-species phylogenetic distance matrix from a tree. only deal with relatively small dataset.

Usage

pdist.p(tree, nworker = 4, memory.G = 50, silent = FALSE, time.count = FALSE)

Arguments

tree	phylogenetic tree, an object of class "phylo".
nworker	for parallel computing the tree paths. a positive integer (in which case that number of copies is run on localhost). default is 4, means 4 threads will be run.
memory.G	numeric, to set the memory size as you need, so that calculation of large tree will not be limited by physical memory. unit is Gb. default is 50Gb
silent	logic, whether to show messages. Default is FALSE, thus all messages will be showed.
time.count	logic, whether to count calculation time, default is FALSE.

Details

The cophenetic distance between each pair of taxa is calculated (Sokal and Rohlf 1962). Modified from the function "cophenetic" in package "ape" (Paradis & Schliep 2018), this function can calculate pairwise distance from phylogenetic tree quickly by parallel computing. If the tree has too many tips (taxa), please use another function pdist.big designed for large datasets.

Value

Output is a data.frame object, a square matrix of pairwise phylogenetic distances. Row names are the same as column names, indicating taxa IDs.

Note

Version 1: 2021.9.24

Author(s)

Daliang Ning

References

Sokal, R. R. & Rohlf, F. J.. (1962). The comparison of dendrograms by objective methods. Taxon, 11:33-40

Paradis, E. & Schliep, K. (2018). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.

See Also

pdist.big

Examples

data("example.data")
tree=example.data$tree
nworker=2 # parallel computing thread number
pd=pdist.p(tree = tree, nworker = nworker)

iCAMP documentation built on June 1, 2022, 9:08 a.m.