RandomSectorialSearchOptions: Set options for a random sectorial search

In paravian/nitro: Integration of TNT in R

Set options for a random sectorial search

Description

RandomSectorialSearchOptions is an R6 class that defines the set of options required to perform sectorial searching analyses in nitro.

Super class

nitro::AbstractSectorialSearchOptions -> RandomSectorialSearchOptions

Active bindings

min_size

An integer value indicating the minimum size of random selections. If NULL (the default), this value will be automatically set according to the number of taxa in the matrix when used with a "TreeAnalysis" object.

max_size

An integer value indicating the maximum size of random selections. If NULL (the default), this value will be automatically set according to the number of taxa in the matrix when a new "TreeAnalysis" object is initialized.

selection_factor

An integer value indicating the maximum number of random selections for the currently active taxa.

increase

An integer value indicating the factor to increase the size of random selections if enough selection of the current size have been completed.

small_starts

An integer value indicating the number of random addition sequence plus tree-bisection reconnection swaps to perform for random selections below min_size.

Methods

Public methods

• RandomSectorialSearchOptions$new()

• RandomSectorialSearchOptions$print()

• RandomSectorialSearchOptions$queue()

• RandomSectorialSearchOptions$clone()

---

Method new()

Usage

RandomSectorialSearchOptions$new(
  min_size = NULL,
  max_size = NULL,
  selection_factor = 50,
  increase = 100,
  small_starts = 3,
  buffer = TRUE,
  slack = 0
)

Arguments

min_size

An integer value indicating the minimum size of random selections. If left as 0 (the default), this value will be automatically set according to the number of taxa in the matrix when a new "TreeAnalysis" object is initialized.

max_size

An integer value indicating the maximum size of random selections. If left at 0 (the default), this value will be automatically set according to the number of taxa in the matrix when a new "TreeAnalysis" object is initialized.

selection_factor

An integer value indicating the maximum number of random selections for the currently active taxa.

increase

An integer value indicating the factor to increase the size of random selections if enough selection of the current size have been completed.

small_starts

An integer value indicating the number of random addition sequence plus tree-bisection reconnection swaps to perform for random selections below min_size.

buffer

A logical value indicating whether to use an independent

slack

An integer value indicating the percentage to increase the available memory during searches.

---

Method print()

Usage

RandomSectorialSearchOptions$print(...)

Arguments

...

Ignored.

---

Method queue()

Usage

RandomSectorialSearchOptions$queue(set_only = FALSE)

Arguments

set_only

A logical indicating whether to instruct the command to execute immediately (TRUE) or set the variables for future execution FALSE.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

RandomSectorialSearchOptions$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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