BranchSwappingOptions: Define a branch swapping analysis
In paravian/nitro: Integration of TNT in R
BranchSwappingOptions R Documentation
Define a branch swapping analysis
Description
BranchSwappingOptions is an R6 class that defines the set of options
for performing a branch sweapping phylogenetic analysis with replications
in nitro.
Active bindings
replicationsAn integer value indicating the number of replications.
hold_repAn integer value indicating the maximum number of trees to
retain during each replication.
keep_allA logical value indicating whether to retain all generated
trees from each replication regardless of length.
Methods
Public methods
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Method new()
Usage
BranchSwappingOptions$new(replications = 10, hold_rep = 10, keep_all = FALSE)
Arguments
replicationsAn integer value indicating the number of replications.
hold_repAn integer value indicating the maximum number of trees to
retain during each replication.
keep_allA logical value indicating whether to retain all generated
trees from each replication regardless of length.
Method print()
Usage
BranchSwappingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
BranchSwappingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
BranchSwappingOptions$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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| BranchSwappingOptions | R Documentation |
Define a branch swapping analysis
Description
BranchSwappingOptions is an R6 class that defines the set of options
for performing a branch sweapping phylogenetic analysis with replications
in nitro.
Active bindings
replicationsAn integer value indicating the number of replications.
hold_repAn integer value indicating the maximum number of trees to retain during each replication.
keep_allA logical value indicating whether to retain all generated trees from each replication regardless of length.
Methods
Public methods
Method new()
Usage
BranchSwappingOptions$new(replications = 10, hold_rep = 10, keep_all = FALSE)
Arguments
replicationsAn integer value indicating the number of replications.
hold_repAn integer value indicating the maximum number of trees to retain during each replication.
keep_allA logical value indicating whether to retain all generated trees from each replication regardless of length.
Method print()
Usage
BranchSwappingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
BranchSwappingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
BranchSwappingOptions$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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