[R-sig-phylo] Nodal values

tgarland at ucr.edu tgarland at ucr.edu
Tue Feb 12 21:05:18 CET 2008


Exactly.  Also, some have referred to the nodes from the contrasts 
algebra as "local parsimony" estimates because they consider only 
the descendants, not any ancestors.  When you consider the root 
(basal) node of a tree, ALL terminal taxa are descendants, so in 
that special case the contrasts algebra yields a "global parsimony" 
estimate (i.e., an estimated based on all of the data on the tree).

Ted

---- Original message ----

  Date: Tue, 12 Feb 2008 11:44:47 -0800
  From: Joe Felsenstein <joe at gs.washington.edu>
  Subject: [R-sig-phylo]  Nodal values
  To: r-sig-phylo at r-project.org
  >
  >Just to clarify, Ted had noted that
  >
  >> ... note that the nodal values used when computing
  Felsenstein's
  >> (1985) phylogenetically independent contrasts are
  different, except
  >> at the base of a rooted tree.
  >
  >People often mistakenly assume that the nodal values used
  in the
  >contrasts calculation are themselves the best possible
  estimates of what
  >the phenotypes were at those nodes, and they go around
  confidently
  >declaring that the contrasts are contrasts between
  reconstructed ancestral
  >phenotypes. As Ted notes, they aren't best
  reconstructions of those (the nodal
  >values can be regarded as reconstructions, but not ones
  that use all the data).
  >Nevertheless they are the proper numbers to use in the
  contrasts
  >calculation -- Ted is not arguing that they are wrong for
  that.
  >
  >Joe
  >----
  >Joe Felsenstein joe at gs.washington.edu
  > Department of Genome Sciences and Department of Biology,
  > University of Washington, Box 355065, Seattle, WA
  98195-5065 USA
  >
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  >R-sig-phylo at r-project.org
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