Prepare data for Profile Parsimony
PrepareDataProfile(dataset, precision = 1e+06, warn = TRUE)PrepareDataIW(dataset)
dataset of class phyDat
number of random trees to generate when calculating Profile curves. With 22 tokens (taxa): - Increasing precision from 4e+05 to 4e+06 reduces error by a mean of 0.005 bits for each step after the first (max = 0.11 bits, sd=0.017 bits) - Increasing precision from 1e+06 to 4e+06 reduces error by a mean of 0.0003 bits for each step after the first (max = 0.046 bits, sd=0.01 bits)
Boolean (TRUE/FALSE): display warnings when concavity
functions are generated by approximation.
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.
split.sizes: The size of the splits implied by each character
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