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
Ambiguous tokens will be treated as fully ambiguous
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.
dataset of class
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
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
PrepareDataIW(): Prepare data for implied weighting
data('congreveLamsdellMatrices') dataset <- congreveLamsdellMatrices[] PrepareDataProfile(dataset) #> 22 sequences with 55 character and 55 different site patterns. #> The states are 0 1