PrepareDataProfile {TreeSearch} | R Documentation |
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 |
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 vectorc("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)