RatchetOptions: Set options for parsimony ratchet
In paravian/nitro: Integration of TNT in R
RatchetOptions R Documentation
Set options for parsimony ratchet
Description
RatchetOptions is an R6 class that defines the set of options
for performing a parsimony ratchet phylogenetic analysis in nitro.
Active bindings
iterationsAn integer value indicating the number of iterations.
replacementsAn integer value indicating the number of
replacements (i.e., accepted tree rearrangements) to perform in each
perturbation phase.
prob_upAn integer value indicating the probability of
upweighting a character.
prob_downAn integer value indicating the probability of
downweighting a character.
Methods
Public methods
Method new()
Usage
RatchetOptions$new(
iterations = 50,
replacements = 40,
prob_up = 4,
prob_down = 4
)
Arguments
iterationsAn integer value indicating the number of iterations.
replacementsAn integer value indicating the number of
replacements (i.e., accepted tree rearrangements) to perform in each
perturbation phase.
prob_upAn integer value indicating the probability of
upweighting a character.
prob_downAn integer value indicating the probability of
downweighting a character.
Method print()
Usage
RatchetOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
RatchetOptions$queue(set_only = FALSE)
Arguments
set_onlyA logical indicating whether to instruct the command to
execute immediately (TRUE) or set the variables for future
execution (FALSE).
Method clone()
The objects of this class are cloneable with this method.
Usage
RatchetOptions$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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| RatchetOptions | R Documentation |
Set options for parsimony ratchet
Description
RatchetOptions is an R6 class that defines the set of options
for performing a parsimony ratchet phylogenetic analysis in nitro.
Active bindings
iterationsAn integer value indicating the number of iterations.
replacementsAn integer value indicating the number of replacements (i.e., accepted tree rearrangements) to perform in each perturbation phase.
prob_upAn integer value indicating the probability of upweighting a character.
prob_downAn integer value indicating the probability of downweighting a character.
Methods
Public methods
Method new()
Usage
RatchetOptions$new( iterations = 50, replacements = 40, prob_up = 4, prob_down = 4 )
Arguments
iterationsAn integer value indicating the number of iterations.
replacementsAn integer value indicating the number of replacements (i.e., accepted tree rearrangements) to perform in each perturbation phase.
prob_upAn integer value indicating the probability of upweighting a character.
prob_downAn integer value indicating the probability of downweighting a character.
Method print()
Usage
RatchetOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
RatchetOptions$queue(set_only = FALSE)
Arguments
set_onlyA logical indicating whether to instruct the command to execute immediately (
TRUE) or set the variables for future execution (FALSE).
Method clone()
The objects of this class are cloneable with this method.
Usage
RatchetOptions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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