PrepareDataProfile: Prepare data for Profile Parsimony
Description
Calculates profiles for each character in a dataset. Will also simplify
characters, with a warning, where they are too complex for the present
implementation of profile parsimony:
inapplicable tokens will be replaced with the ambiguous token
(i.e. - → ?);
Ambiguous tokens will be treated as fully ambiguous
(i.e. {02} → ?)
Where more than two states are informative (i.e. unambiguously present in
more than one taxon), states beyond the two most informative will be
ignored.
Usage
PrepareDataProfile(dataset)
PrepareDataIW(dataset)
Value
An object of class phyDat, with additional attributes.
PrepareDataProfile adds the attributes:
info.amounts: details the information represented by each
character when subject to N additional steps.
informative: logical specifying which characters contain any
phylogenetic information.
bootstrap: The character vector
c("info.amounts", "split.sizes"), indicating attributes to sample
when bootstrapping the dataset (e.g. in Ratchet searches).
PrepareDataIW adds the attribute:
min.length: The minimum number of steps that must be present in each
transformation series.
Arguments
dataset
dataset of class phyDat
Functions
PrepareDataIW(): Prepare data for implied weighting
Author
Martin R. Smith; written with reference to
phangorn:::prepareDataFitch()
See Also
Other profile parsimony functions:
Carter1(),
StepInformation(),
WithOneExtraStep(),
profiles