ImpliedWeightingOptions: Set options for implied weighting
In paravian/nitro: Integration of TNT in R
ImpliedWeightingOptions R Documentation
Set options for implied weighting
Description
ImpliedWeightingOptions is an R6 class that defines the set of options
for using (extended) implied weighting with phylogenetic analyses in
nitro.
Active bindings
kA numeric value indicating the concavity constant to apply
during an implied weights analysis. When multi_k is
TRUE, k represents the concavity for a character with
no missing entries and serves as the basis for calculating per-site
concavity constants.
multi_kA logical value indicating whether each character will be
given an independent concavity constant based on the value of k
during an implied weights analysis.
proportionA numeric value indicating the proportion of homoplasy
missing values are assumed to have under implied weighting. This
parameter is only valid when multi_k is TRUE. A
proportion of 0 is equivalent to standard implied weighting, with
multi_k set as FALSE.
max_ratioA numeric value indicating the maximum acceptable ratio
between two k values when multiple concavity constants are used (i.e.,
when multi_k is TRUE). A maximum ratio of 1 is
equivalent to standard implied weighting, with multi_k set as
FALSE.
Methods
Public methods
-
-
-
-
Method new()
Usage
ImpliedWeightingOptions$new(
k = 3,
multi_k = FALSE,
proportion = 0.5,
max_ratio = 5
)
Arguments
kA numeric value indicating the concavity constant to apply during
an implied weights analysis. When multi_k is TRUE, k
represents the concavity for a character with no missing entries and
serves as the basis for calculating per-site concavity constants.
multi_kA logical value indicating whether each character will be
given an independent concavity constant based on the value of k
during an implied weights analysis.
proportionA numeric value indicating the proportion of homoplasy
missing values are assumed to have under implied weighting. This parameter
is only valid when multi_k is TRUE. A proportion of 0 is
equivalent to standard implied weighting, with multi_k set as
FALSE.
max_ratioA numeric value indicating the maximum acceptable ratio
between two k values when multiple concavity constants are used (i.e.,
when multi_k is TRUE). A maximum ratio of 1 is equivalent
to standard implied weighting, with multi_k set as FALSE.
Method print()
Usage
ImpliedWeightingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
ImpliedWeightingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
ImpliedWeightingOptions$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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| ImpliedWeightingOptions | R Documentation |
Set options for implied weighting
Description
ImpliedWeightingOptions is an R6 class that defines the set of options
for using (extended) implied weighting with phylogenetic analyses in
nitro.
Active bindings
kA numeric value indicating the concavity constant to apply during an implied weights analysis. When
multi_kisTRUE,krepresents the concavity for a character with no missing entries and serves as the basis for calculating per-site concavity constants.multi_kA logical value indicating whether each character will be given an independent concavity constant based on the value of
kduring an implied weights analysis.proportionA numeric value indicating the proportion of homoplasy missing values are assumed to have under implied weighting. This parameter is only valid when
multi_kisTRUE. A proportion of 0 is equivalent to standard implied weighting, withmulti_kset asFALSE.max_ratioA numeric value indicating the maximum acceptable ratio between two k values when multiple concavity constants are used (i.e., when
multi_kisTRUE). A maximum ratio of 1 is equivalent to standard implied weighting, withmulti_kset asFALSE.
Methods
Public methods
Method new()
Usage
ImpliedWeightingOptions$new( k = 3, multi_k = FALSE, proportion = 0.5, max_ratio = 5 )
Arguments
kA numeric value indicating the concavity constant to apply during an implied weights analysis. When
multi_kisTRUE,krepresents the concavity for a character with no missing entries and serves as the basis for calculating per-site concavity constants.multi_kA logical value indicating whether each character will be given an independent concavity constant based on the value of
kduring an implied weights analysis.proportionA numeric value indicating the proportion of homoplasy missing values are assumed to have under implied weighting. This parameter is only valid when
multi_kisTRUE. A proportion of 0 is equivalent to standard implied weighting, withmulti_kset asFALSE.max_ratioA numeric value indicating the maximum acceptable ratio between two k values when multiple concavity constants are used (i.e., when
multi_kisTRUE). A maximum ratio of 1 is equivalent to standard implied weighting, withmulti_kset asFALSE.
Method print()
Usage
ImpliedWeightingOptions$print(...)
Arguments
...Ignored.
Method queue()
Usage
ImpliedWeightingOptions$queue(...)
Arguments
...Ignored.
Method clone()
The objects of this class are cloneable with this method.
Usage
ImpliedWeightingOptions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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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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