DiscreteMatrix: Discrete character matrix

In paravian/nitro: Integration of TNT in R

Discrete character matrix

Description

DiscreteMatrix is an R6 class that contains a discrete character matrix and functions for modifying character activity and ordering.

Super class

nitro::AbstractCharacterMatrix -> DiscreteMatrix

Active bindings

data_type

The type of discrete character data contained in the matrix.

n_states

The number of unique states contained in the matrix.

symbols

The unique set of discrete characters contained in the matrix.

ordered

A numeric vector indicating which characters to mark as ordered.

Methods

Public methods

• DiscreteMatrix$new()

• DiscreteMatrix$print()

• DiscreteMatrix$queue()

• DiscreteMatrix$clone()

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Method new()

Usage

DiscreteMatrix$new(data, ordered = NULL, inactive = NULL)

Arguments

data

A phyDat discrete character matrix.

ordered

A numeric vector indicating which characters to mark as ordered.

inactive

A numeric vector indicating which characters to mark as inactive.

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Method print()

Usage

DiscreteMatrix$print(...)

Arguments

...

Ignored.

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Method queue()

Generate the command queue

Usage

DiscreteMatrix$queue(...)

Arguments

...

Ignored.

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Method clone()

The objects of this class are cloneable with this method.

Usage

DiscreteMatrix$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

paravian/nitro documentation built on Jan. 17, 2025, 11:21 p.m.