get_gower_dist: Compute Gower distances between characters

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Compute Gower distances between characters

Description

Computes Gower distance between characters from a phylogenetic data matrix.

Usage

get_gower_dist(x, numeric = FALSE)

Arguments

x	A phylogenetic data matrix in Nexus (.nex) format, or in any other data frame or matrix format with a column for each character and terminal taxa as rows, which will be read using ape::read.nexus.data. The data cannot include polymorphisms.
numeric	Whether to treat the values contained in the x as numeric or categorical. If FALSE (default), features will be considered categorical; if TRUE, they will be considered numeric.

Value

The Gower distance matrix.

Author(s)

This function uses code adapted from StatMatch::gower.dist() written by Marcello D'Orazio.

See Also

vignette("char-part") for the use of this function as part of an analysis pipeline.

Examples

# See vignette("char-part") for how to use this
# function as part of an analysis pipeline

# Load example phylogenetic data matrix
data("characters")

# Create distance matrix
Dmatrix <- get_gower_dist(characters)

# Reading data matrix as numeric data
Dmatrix <- get_gower_dist(characters, numeric = TRUE)

EvoPhylo documentation built on Nov. 4, 2022, 1:06 a.m.