TreeFusingOptions: Set options for tree fusing
In paravian/nitro: Integration of TNT in R
TreeFusingOptions R Documentation
Set options for tree fusing
Description
TreeFusingOptions is an R6 class that defines the set of parameters
required for performing tree fusing operations in nitro.
Active bindings
roundsAn integer value indicating the number of tree-fusing rounds
to perform.
exchange_equalA logical value indicating whether to accept exchanges
of equal score.
start_bestA logical value indicating whether to use the best tree to
start tree-fusing.
keep_allA logical value indicating whether to keep all trees found
instead of only the best trees.
accept_allA logical value indicating whether to accept all exchanges
rather than only those that improve the best score.
swapA logical value indicating whether to perform tree-bisection
reconnection swapping after exchanging clades.
Methods
Public methods
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Method new()
Usage
TreeFusingOptions$new(
rounds = 5,
exchange_equal = FALSE,
start_best = TRUE,
keep_all = TRUE,
accept_all = TRUE,
swap = TRUE
)
Arguments
roundsAn integer value indicating the number of tree-fusing rounds
to perform.
exchange_equalA logical value indicating whether to accept exchanges
of equal score.
start_bestA logical value indicating whether to use the best tree to
start tree-fusing.
keep_allA logical value indicating whether to keep all trees found
instead of only the best trees.
accept_allA logical value indicating whether to accept all exchanges
rather than only those that improve the best score.
swapA logical value indicating whether to perform tree-bisection
reconnection swapping after exchanging clades.
Method print()
Usage
TreeFusingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
TreeFusingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
TreeFusingOptions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
paravian/nitro documentation built on Jan. 17, 2025, 11:21 p.m.
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| TreeFusingOptions | R Documentation |
Set options for tree fusing
Description
TreeFusingOptions is an R6 class that defines the set of parameters
required for performing tree fusing operations in nitro.
Active bindings
roundsAn integer value indicating the number of tree-fusing rounds to perform.
exchange_equalA logical value indicating whether to accept exchanges of equal score.
start_bestA logical value indicating whether to use the best tree to start tree-fusing.
keep_allA logical value indicating whether to keep all trees found instead of only the best trees.
accept_allA logical value indicating whether to accept all exchanges rather than only those that improve the best score.
swapA logical value indicating whether to perform tree-bisection reconnection swapping after exchanging clades.
Methods
Public methods
Method new()
Usage
TreeFusingOptions$new( rounds = 5, exchange_equal = FALSE, start_best = TRUE, keep_all = TRUE, accept_all = TRUE, swap = TRUE )
Arguments
roundsAn integer value indicating the number of tree-fusing rounds to perform.
exchange_equalA logical value indicating whether to accept exchanges of equal score.
start_bestA logical value indicating whether to use the best tree to start tree-fusing.
keep_allA logical value indicating whether to keep all trees found instead of only the best trees.
accept_allA logical value indicating whether to accept all exchanges rather than only those that improve the best score.
swapA logical value indicating whether to perform tree-bisection reconnection swapping after exchanging clades.
Method print()
Usage
TreeFusingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
TreeFusingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
TreeFusingOptions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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