Compute Gower distances between characters

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.

Author

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

Value

The Gower distance matrix.

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)
#> Warning: NAs introduced by coercion; some values could not be converted to numbers.