TreeSearch (version 0.3.2)

MinimumSteps: Minimum steps

Description

The smallest number of steps that a character can take on any tree.

Usage

MinimumSteps(states)

Arguments

states

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 means that the tip may have tokens 0, 1 or 3 (as 11 = 2^0 + 2^1 + 2^3). As the minimum steps can be found when inapplicables occur together, inapplicable tokens can be denoted as ?s or with the integer 0 (not 2^0). Tokens that are ambiguous for an inapplicable and an applicable state are not presently supported.

Value

An integer specifying the minimum number of steps that the character must contain.

Examples

# NOT RUN {
{
  data('inapplicable.datasets')
  myPhyDat <- inapplicable.phyData[[4]] # or as.phyDat(read.nexus.data('filepath'))
  class(myPhyDat) # phyDat object
  
  # Convert list of character codings to an array
  myData <- vapply(myPhyDat, I, myPhyDat[[1]])
  
  # Convert phyDat's representation of states to binary
  myContrast <- attr(myPhyDat, 'contrast')
  tokens <- colnames(myContrast)
  binaryContrast <- integer(length(tokens))
  tokenApplicable <- tokens != '-'
  binaryContrast[tokenApplicable] <- 2 ^ (seq_len(sum(tokenApplicable)) - 1)
  binaryValues <- apply(myContrast, 1, 
    function (row) sum(binaryContrast[as.logical(row)]))
  myStates <- matrix(binaryValues[myData], nrow=nrow(myData),
                     ncol=ncol(myData), dimnames=dimnames(myData))
 
  # Finally, work out minimum steps 
  apply(myStates, 1, MinimumSteps)
  
}

# }