BranchSupportOptions: Set options for branch support calculation
In paravian/nitro: Integration of TNT in R
BranchSupportOptions R Documentation
Set options for branch support calculation
Description
BranchSupportOptions is an R6 class that defines options for calculating
decay indices.
Active bindings
index_typeA character vector indicating the type of index to
calculate. Options are either absolute (default) or
relative.
group_loss_costA character vector indicating what cost to use
for losing a group in a suboptimal tree.
suboptimal_stepsAn integer value indicating the maximum absolute
fit difference (i.e., length difference) of suboptimal trees to use
for calculating supports.
relative_suboptimal_fitA numeric value indicating the maximum
relative fit difference of suboptimal trees to use for calculating
supports.
group_collapse_valueAn integer value indicating the support value
below which groups in the tree will be collapsed. Can be zero or a
negative number.
Methods
Public methods
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Method new()
Usage
BranchSupportOptions$new(
index_type = "absolute",
group_loss_cost = "standard",
group_collapse_value = 1,
suboptimal_steps = 10,
relative_suboptimal_fit = NULL
)
Arguments
index_typeA character vector indicating the type of index to
calculate. Options are either absolute (default) or
relative.
group_loss_costA character vector indicating what cost to use
for losing a group in a suboptimal tree.
group_collapse_valueAn integer value indicating the support value
below which groups in the tree will be collapsed. Can be zero or a
negative number.
suboptimal_stepsAn integer value indicating the maximum length
of suboptimal trees to keep during branch swapping.
relative_suboptimal_fitA numeric value indicating the maximum
relative fit difference of suboptimal trees to use for calculating
supports.
Method print()
Usage
BranchSupportOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
BranchSupportOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
BranchSupportOptions$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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| BranchSupportOptions | R Documentation |
Set options for branch support calculation
Description
BranchSupportOptions is an R6 class that defines options for calculating
decay indices.
Active bindings
index_typeA character vector indicating the type of index to calculate. Options are either
absolute(default) orrelative.group_loss_costA character vector indicating what cost to use for losing a group in a suboptimal tree.
suboptimal_stepsAn integer value indicating the maximum absolute fit difference (i.e., length difference) of suboptimal trees to use for calculating supports.
relative_suboptimal_fitA numeric value indicating the maximum relative fit difference of suboptimal trees to use for calculating supports.
group_collapse_valueAn integer value indicating the support value below which groups in the tree will be collapsed. Can be zero or a negative number.
Methods
Public methods
Method new()
Usage
BranchSupportOptions$new( index_type = "absolute", group_loss_cost = "standard", group_collapse_value = 1, suboptimal_steps = 10, relative_suboptimal_fit = NULL )
Arguments
index_typeA character vector indicating the type of index to calculate. Options are either
absolute(default) orrelative.group_loss_costA character vector indicating what cost to use for losing a group in a suboptimal tree.
group_collapse_valueAn integer value indicating the support value below which groups in the tree will be collapsed. Can be zero or a negative number.
suboptimal_stepsAn integer value indicating the maximum length of suboptimal trees to keep during branch swapping.
relative_suboptimal_fitA numeric value indicating the maximum relative fit difference of suboptimal trees to use for calculating supports.
Method print()
Usage
BranchSupportOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
BranchSupportOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
BranchSupportOptions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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