MonophylyConstraintOptions: Set constraints on monophyly

In paravian/nitro: Integration of TNT in R

Set constraints on monophyly

Description

MonophylyConstraintOptions is an R6 class that sets options for tree searches with constraints on monophyly.

Super class

nitro::ConstraintBaseOptions -> MonophylyConstraintOptions

Active bindings

fixed_otus

A logical vector indicating which OTUs from the matrix to assign as a fixed constraint.

floating_otus

An optional logical vector indicating which OTUs from the matrix to assign as floating constraints.

Methods

Public methods

• MonophylyConstraintOptions$new()

• MonophylyConstraintOptions$print()

• MonophylyConstraintOptions$queue()

• MonophylyConstraintOptions$clone()

---

Method new()

Usage

MonophylyConstraintOptions$new(
  fixed_otus,
  floating_otus = NULL,
  is_positive = TRUE
)

Arguments

fixed_otus

A character vector indicating which OTUs from the matrix to assign as a fixed constraint.

floating_otus

An character logical vector indicating which OTUs from the matrix to assign as floating constraints.

is_positive

A logical value indicating whether the constraint is positive (TRUE) or negative (FALSE).

---

Method print()

Usage

MonophylyConstraintOptions$print(...)

Arguments

...

Ignored.

---

Method queue()

Usage

MonophylyConstraintOptions$queue(...)

Arguments

...

Ignored.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MonophylyConstraintOptions$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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