PrepareDataProfile | R Documentation |
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)
dataset |
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
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.
PrepareDataIW()
: Prepare data for implied weighting
Martin R. Smith; written with reference to
phangorn:::prepareDataFitch()
Other profile parsimony functions:
Carter1()
,
StepInformation()
,
WithOneExtraStep()
,
profiles
data("congreveLamsdellMatrices")
dataset <- congreveLamsdellMatrices[[42]]
PrepareDataProfile(dataset)
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