apply.NA: Apply inapplicable characters to a matrix.

View source: R/morpho.utilities.R

apply.NAR Documentation

Apply inapplicable characters to a matrix.

Description

Apply inapplicable characters to discrete morphological matrix.

Usage

apply.NA(matrix, NAs, tree, invariant = FALSE, verbose = FALSE)

Arguments

matrix

A discrete morphological matrix.

NAs

Either a numeric value of how many characters to make inapplicable or vector of characters inapplicability source (either "character" or "clade"; see details). The length of this vector must be at maximum half the total number of characters.

tree

If any inapplicable source is "clade", a tree from where to select the clades.

invariant

Whether to allow invariant sites among the characters with inapplicable data. If invariant = FALSE the algorithm will try to remove such characters (if possible).

verbose

Whether to be verbose or not.

Details

If the NAs argument is a numeric value n, generates n characters with inapplicable data based on the "clade" source.

The NAs argument intakes a vector of character inapplicability source rendering a number of characters inapplicable using the following sources:

"character" draws inapplicable characters directly from the character matrix, ignoring the phylogeny (i.e. for a random character X, an other random character Y will have inapplicable characters for each character states 0 for character X).

"clade" draws inapplicable characters from the phylogeny: it will randomly apply inapplicable characters states for some characters by randomly selecting clades from the provided tree. The algorithm randomly assigns an inapplicable token for this character for all taxa in this clade or all taxa outside this clade.

For example NAs = c(rep("character", 2), rep("clade", 2)) will generate 4 characters with inapplicable data, two using previous characters and two other using random clades.

Author(s)

Thomas Guillerme

See Also

sim.morpho

Examples

set.seed(4)
## A random tree with 15 tips
tree <- rcoal(15)
## setting up the parameters
my_rates = c(rgamma, rate = 10, shape = 5)
my_substitutions = c(runif, 2, 2)

## A Mk matrix (10*50)
matrixMk <- sim.morpho(tree, characters = 100, model = "ER",
     states = c(0.85, 0.15), rates = my_rates, invariant = FALSE)

## Setting the number and source of inapplicable characters
my_inapplicables <- c(rep("character", 5), rep("clade", 5))

## Apply some inapplicable characters to the matrix
matrix <- apply.NA(matrixMk, my_inapplicables, tree, verbose = TRUE)


dispRity documentation built on May 29, 2024, 9:40 a.m.