DrivenSearchOptions: Set options for driven searches

In paravian/nitro: Integration of TNT in R

Set options for driven searches

Description

DrivenSearchOptions is an R6 class that defines the set of parameters required to perform a driven search in nitro.

Active bindings

replications

An integer value indicating the number of replications.

hits

An integer value indicating the number of times the shortest tree must be found on consecutive re-runs of the analysis before stopping.

consense_times

An integer value indicating the number of times to consense until the consensus is stablilised.

keep_all

A logical value indicating whether to retain all generated trees from each replication regardless of length.

multiply

A logical value indicating whether to find additional trees by fusing suboptimal trees with optimal trees.

sectorial_search

One or a list of objects of inheriting "SectorialSearchBaseOptions".

tree_fusing

An object of class "TreeFusingOptions".

tree_hybridizing

An object of class "TreeHybridizingOptions".

tree_drifting

An object of class "TreeDriftingOptions".

ratchet

An object of class "RatchetOptions".

Methods

Public methods

• DrivenSearchOptions$new()

• DrivenSearchOptions$print()

• DrivenSearchOptions$queue()

• DrivenSearchOptions$clone()

---

Method new()

Usage

DrivenSearchOptions$new(
  replications = 4,
  hits = 1,
  consense_times = 0,
  keep_all = FALSE,
  multiply = TRUE,
  sectorial_search = NULL,
  tree_fusing = NULL,
  tree_hybridizing = NULL,
  tree_drifting = NULL,
  ratchet = NULL
)

Arguments

replications

an integer value indicating the number of replications.

hits

An integer value indicating the number of times the shortest tree must be found on consecutive re-runs of the analysis before stopping.

consense_times

An integer value indicating the number of times to consense until the consensus is stablilised.

keep_all

A logical value indicating whether to retain all generated trees from each replication regardless of length. This has a different meaning when hits = 1 and when hits > 1. When hits = 1, it is trees from each of the RAS + TBR + SS or DFT or RAT, in addition to the trees resulting from fusing those. When hits > 1, then it means the trees resulting from fusing the initial starting trees for each of starting points.

multiply

A logical value indicating whether to find additional trees by fusing suboptimal trees with optimal trees.

sectorial_search

A list of objects of inheriting "SectorialSearchBaseOptions".

tree_fusing

An object of class "TreeFusingOptions".

tree_hybridizing

An object of class "TreeHybridizingOptions".

tree_drifting

An object of class "TreeDriftingOptions".

ratchet

An object of class "RatchetOptions".

---

Method print()

Usage

DrivenSearchOptions$print(...)

Arguments

...

Ignored.

---

Method queue()

Usage

DrivenSearchOptions$queue(...)

Arguments

...

Ignored.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DrivenSearchOptions$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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