Contml: Continuous characters

[pascalangst]

Hi @liamrevell

Quick question, why is Rcontml() using continuous characters as a default (and not gene frequencies)?

https://github.com/liamrevell/Rphylip/blob/eee8c6eff145aee4030fb6eb9279e204ddcab5de/Rphylip/R/Rphylip.R#L2593

Those are the default parameters for phylip when I'm using Rcontml():

Continuous character Maximum Likelihood method version 3.697

Settings for this run:
  U                       Search for best tree?  Yes
  C  Gene frequencies or continuous characters?  Continuous characters
  O                              Outgroup root?  No, use as outgroup species 1
  G                      Global rearrangements?  Yes
  J           Randomize input order of species?  Yes (seed=   59753, 10 times)
  M                 Analyze multiple data sets?  No
  0         Terminal type (IBM PC, ANSI, none)?  ANSI
  1          Print out the data at start of run  No
  2        Print indications of progress of run  Yes
  3                              Print out tree  Yes
  4             Write out trees onto tree file?  Yes

From phylip the manual:

If you are going to use Contml to model evolution of continuous characters, then you should at least make some attempt to remove genetic correlations between the characters (usually all one can do is remove phenotypic correlations by transforming the characters so that there is no within-population covariance and so that the within-population variances of the characters are equal -- this is equivalent to using Canonical Variates). However, this will only guarantee that one has removed phenotypic covariances between characters. Genetic covariances could only be removed by knowing the coheritabilities of the characters, which would require genetic experiments, and selective covariances (covariances due to covariation of selection pressures) would require knowledge of the sources and extent of selection pressure in all variables.