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 of class phyDat
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
Other profile parsimony functions:
Carter1()
,
StepInformation()
,
WithOneExtraStep()
,
profiles
data("congreveLamsdellMatrices")
dataset <- congreveLamsdellMatrices[[42]]
PrepareDataProfile(dataset)
#> 22 sequences with 55 character and 55 different site patterns.
#> The states are 0 1