TreeAnalysis: Define tree searches

In paravian/nitro: Integration of TNT in R

Define tree searches

Description

TreeAnalysis is an R6 class that stores the configuration for a tree analysis, including the character-taxon matrix, taxon activity, character weighting and constraints on monophyly.

Active bindings

discrete_matrix

A "DiscreteMatrix" object.

continuous_matrix

A "ContinuousMatrix" object.

method

An object that contains configuration options for a tree analysis method.

inactive_taxa

A character vector indicating the taxa to be inactivated.

outgroup

A single character vector indicating the taxon to be the outgroup.

zlb_rule

A character vector indicating the rule for handling zero length branches. The options are:

• maximum: collapse an interior branch of the maximum possible length of the branch is zero;

• identical_states: only collapse zero length branches if ancestor and descendant states are the same;

• minimum: collapse an interior branch if the minimum possible length of the branch is zero (default);

• discard_tree: discard all trees that must contain a zero length branch;

• spr: collapse an interior branch using subtree pruning and reconnection (SPR) operations; and

• tbr: collapse an interior branch using tree bisection and reconnection (TBR) operations.

constraints

One or more "MonophylyConstraintOptions" objects.

weighting

An object containing configuration options for character weighting.

start_trees

A phylo or multiPhylo of trees to load prior to starting the tree analysis.

hold

An integer indicating the number of trees to hold in TNT's tree buffer.

max_ram

A numeric indicating the number of (binary) megabytes to allocate for use by TNT.

timeout

A positive integer indicating the number of seconds to allow a search to run for before terminating.

Methods

Public methods

• TreeAnalysis$new()

• TreeAnalysis$print()

• TreeAnalysis$queue()

• TreeAnalysis$run()

• TreeAnalysis$clone()

---

Method new()

Usage

TreeAnalysis$new(
  method,
  discrete_matrix = NULL,
  continuous_matrix = NULL,
  inactive_taxa = NULL,
  outgroup = NULL,
  zlb_rule = "minimum",
  constraints = NULL,
  weighting = NULL,
  start_trees = NULL,
  hold = 100,
  max_ram = 16,
  timeout = NULL
)

Arguments

method

An object that contains configuration options for the tree analysis method.

discrete_matrix

A "DiscreteMatrix" object.

continuous_matrix

A "ContinuousMatrix" object.

inactive_taxa

A character vector indicating the taxa to be inactivated.

outgroup

A single character vector indicating the taxon to be the outgroup.

zlb_rule

An integer indicating the rule for collapsing of zero length branches. The options are:

• maximum: collapse an interior branch of the maximum possible length of the branch is zero;

• identical_states: only collapse zero length branches if ancestor and descendant states are the same;

• minimum: collapse an interior branch if the minimum possible length of the branch is zero (the default); and

• discard_tree: discard all trees that must contain a zero length branch.

• spr: collapse an interior branch using subtree pruning and reconnection (SPR) operations; and

• tbr: collapse an interior branch using tree bisection and reconnection (TBR) operations.

constraints

One or more "MonophylyConstraintOptions" objects.

weighting

An object containing configuration options for character weighting.

start_trees

A phylo or multiPhylo of trees to load prior to starting the tree analysis.

hold

An integer indicating the number of trees to hold in TNTs tree buffer.

max_ram

A numeric indicating the number of (binary) megabytes to allocate for use by TNT.

timeout

A positive integer indicating the number of seconds to allow a search to run for before terminating.

---

Method print()

Usage

TreeAnalysis$print(...)

Arguments

...

Ignored.

---

Method queue()

Usage

TreeAnalysis$queue(...)

Arguments

...

Ignored.

---

Method run()

Usage

TreeAnalysis$run(.envir = parent.frame())

Arguments

.envir

The environment that TNT has been attached to.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TreeAnalysis$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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