Kmultparallel: Parallel implementation of Adams' Kmult

In fruciano/GeometricMorphometricsMix: Miscellaneous functions useful for geometric morphometrics

Parallel implementation of Adams' Kmult

Description

Parallel implementation of Kmult, a measure of phylogenetic signal which is a multivariate equivalent of Blomberg's K

Usage

Kmultparallel(data, trees, ncores = 1, burninpercent = 0, iter = 0)

Arguments

data	data frame with continuous (multivariate) phenotypes, including geometric morphometric data
trees	a multi-phylo object containing a collection of trees
ncores	number of cores to use (default 1; i.e., no parallelization)
burninpercent	percentage of trees in trees to discard as burn-in (by default no tree is discarded)
iter	number of permutations to be used in the permutation test (this should normally be left at the default value of 0)

Details

This is an updated and improved version of the function included in Fruciano et al. 2017. It performs the computation of Adams' Kmult (Adams 2014) in parallel with the aim of facilitating computation on a distribution of trees rather than a single tree This is a very simple parallelization of the code ('embarassingly parallel') which uses internally Adams' published code (to maintain consistency over time). If one wanted to perform a computation of Kmult on a single tree, he/she would be advised to use the version implemented in the package geomorph.

Value

The function outputs a matrix with as many rows as input trees and columns:

Phylogenetic signal (K mult)

Value of Kmult for each tree

p value

p value for the significance of the test (normally not used)

Notice

Under Windows, this implementation needs the package 'parallelsugar' if one wants to run it with multiple cores in parallel. The package 'parallelsugar' can be installed from Github with the command devtools::install_github("nathanvan/parallelsugar") This, in turn, requires the package devtools to be installed. Notice also that the reason why the value of iter is set to 0 by default is that using permutations slows down sensibly the computation and it is of doubtful utility in most cases (as one would get a distribution of p-values not independent from each other). Unless one has a specific use in mind, the suggestion is, then, to keep iter at the default value

Citation

If you use this function please kindly cite both Fruciano et al. 2017 (because you're using this parallelized function) Adams 2014 (because the function computes Adams' Kmult)

References

Adams DC. 2014. A Generalized K Statistic for Estimating Phylogenetic Signal from Shape and Other High-Dimensional Multivariate Data. Systematic Biology 63:685-697.

Fruciano C, Celik MA, Butler K, Dooley T, Weisbecker V, Phillips MJ. 2017. Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets. Ecology and Evolution 7:7034-7046.

fruciano/GeometricMorphometricsMix documentation built on Jan. 31, 2024, 6:24 a.m.