Minimum and Maximum lengths possible for a character

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

Usage

MinimumLength(x, compress = FALSE)

# S3 method for class 'phyDat'
MinimumLength(x, compress = FALSE)

# S3 method for class 'numeric'
MinimumLength(x, compress = NA)

# S3 method for class 'character'
MinimumLength(x, compress = TRUE)

# S3 method for class 'character'
MaximumLength(x, compress = TRUE)

MinimumSteps(x)

MaximumLength(x, compress = TRUE)

# S3 method for class 'numeric'
MaximumLength(x, compress = NA)

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.

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.

Details

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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

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
#> [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