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.

PrepareDataProfile(dataset)

PrepareDataIW(dataset)

## Arguments

dataset

dataset of class phyDat

## 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.

## Functions

• PrepareDataIW: Prepare data for implied weighting

Other profile parsimony functions: Carter1(), StepInformation(), WithOneExtraStep(), profiles

## Author

Martin R. Smith; written with reference to phangorn:::prepareDataFitch()

## Examples

data('congreveLamsdellMatrices')
dataset <- congreveLamsdellMatrices[[42]]
PrepareDataProfile(dataset)
#> 22 sequences with 55 character and 55 different site patterns.
#> The states are 0 1