TreeAnalysisResults: Results of a tree analyses

In paravian/nitro: Integration of TNT in R

Results of a tree analyses

Description

TreeAnalysisResults is an R6 class that contains the results of a tree analysis in nitro.

Active bindings

trees

The trees generated from the analysis of queue.

queue

The CommandQueue object and generated the results.

statistics

The statistics associated with each tree in trees.

Methods

Public methods

• TreeAnalysisResults$new()

• TreeAnalysisResults$print()

• TreeAnalysisResults$clone()

---

Method new()

Usage

TreeAnalysisResults$new(
  phy,
  queue,
  lengths = NULL,
  adjusted_homoplasy_scores = NULL,
  min_length = NULL,
  max_length = NULL,
  tags = NULL
)

Arguments

phy

A multiPhylo object.

queue

A "CommandQueue" object.

lengths

A numeric vector of lengths for trees.

adjusted_homoplasy_scores

A numeric vector of adjusted homoplasy scores for trees.

min_length

A number indicating the minimum possible length for trees given the active characters and taxa.

max_length

A number indicating the maximum possible length for trees given the active characters and taxa.

tags

A data frame containing annotation variables for trees.

---

Method print()

Usage

TreeAnalysisResults$print(...)

Arguments

...

Ignored.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TreeAnalysisResults$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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