PrepareDataProfile: Prepare data for Profile Parsimony

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

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)

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

Author(s)

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

See Also

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

Examples

data("congreveLamsdellMatrices")
dataset <- congreveLamsdellMatrices[[42]]
PrepareDataProfile(dataset)

TreeSearch documentation built on April 11, 2025, 5:49 p.m.