TreeSearch (version 1.5.0)

MinimumLength: Minimum and Maximum lengths possible for a character

Description

The smallest and largest length that a phylogenetic character can attain on any tree.

Usage

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)

Value

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.

Arguments

x

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).

compress

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.

Author

Martin R. Smith ()

Details

Ambiguous inapplicables (e.g. {0, -}) are currently replaced with the plain inapplicable token -, reflecting the current behaviour of Morphy.

See Also

Other tree scoring: CharacterLength(), IWScore(), LengthAdded(), MorphyTreeLength(), TaxonInfluence()

Examples

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

# Minimum length of each character in turn
MinimumLength(myPhyDat)

# Collapse duplicate characters, per phyDat compression
MinimumLength(myPhyDat, compress = TRUE)

# Calculate length of a single character from its textual representation
MinimumLength("-{-1}{-2}{-3}2233")
MaximumLength("----0011")