The smallest and largest length that a phylogenetic character can attain on any tree.
MinimumLength(x, compress = FALSE)
# S3 method for phyDat
MinimumLength(x, compress = FALSE)
# S3 method for numeric
MinimumLength(x, compress = NA)
# S3 method for character
MinimumLength(x, compress = TRUE)
# S3 method for character
MaximumLength(x, compress = TRUE)
MinimumSteps(x)
MaximumLength(x, compress = TRUE)
# S3 method for numeric
MaximumLength(x, compress = NA)An object of class phyDat;
or a string to be coerced to a phyDat object via
TreeTools::StringToPhyDat();
or an integer vector listing the tokens that may be present at each
tip along a single character, with each token represented as a binary digit;
e.g. a value of 11 ( = 2^0 + 2^1 + 2^3) means that
the tip may have tokens 0, 1 or 3.
Inapplicable tokens should be denoted with the integer 0 (not 2^0).
Logical specifying whether to retain the compression of a
phyDat object or to return a vector specifying to each individual
character, decompressed using the dataset's index attribute.
MinimumLength() returns a vector of integers specifying the
minimum number of steps that each character must contain.
MaximumLength() returns a vector of integers specifying the
maximum number of steps that each character can attain in a parsimonious
reconstruction on a tree. Inapplicable tokens are not yet supported.
Ambiguous inapplicable states (e.g. {0, -}) are currently replaced with the
plain inapplicable token -, reflecting the current behaviour of Morphy.
Other tree scoring:
CharacterLength(),
IWScore(),
LengthAdded(),
MorphyTreeLength(),
TaxonInfluence()
data("inapplicable.datasets")
myPhyDat <- inapplicable.phyData[[4]]
# load your own data with
# my.PhyDat <- as.phyDat(read.nexus.data("filepath"))
# or Windows users can select a file interactively using:
# my.PhyDat <- as.phyDat(read.nexus.data(choose.files()))
class(myPhyDat) # phyDat object
#> [1] "phyDat"
# Minimum length of each character in turn
MinimumLength(myPhyDat)
#> [1] 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1
#> [38] 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 2 1 1 2 1 1 4 3 1 1 1 1 2 1
#> [75] 1 1 1 1 1 1 2 4 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
# Collapse duplicate characters, per phyDat compression
MinimumLength(myPhyDat, compress = TRUE)
#> [1] 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1
#> [38] 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 2 1 1 2 1 1 4 3 1 1 1 1 2 1
#> [75] 1 1 1 1 1 1 2 4 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1
# Calculate length of a single character from its textual representation
MinimumLength("-{-1}{-2}{-3}2233")
#> [1] 2
MaximumLength("----0011")
#> [1] 3