You can call any command-line thing from R with system().
Typically I use R to write the control file (e.g. for r8s),
then do something like...
cmdstr = paste("program_name", "-options", "control_file",
"> output.log", sep=" ")
system(cmdstr)
Cheers!
Nick
On 2/22/11 5:42 AM, Scott Chamberl
Minor addition. In Purvis and Garland (1993), we note that you need a
special-case rule for a tree that is one giant soft polytomy, i.e., that you
allow yourself 1 d.f., not zero.
Also, note that all of these corrections to d.f. are approximations.
Cheers,
Ted
Theodore Garland, Jr.
Profess
Hi Popko,
Liam is correct. Answering the second question, I presume your
polytomies involve multiple specimens (individuals) of the same species,
is that right? If so, you do not need to correct for soft politomies;
instead, you may partition the variation within/between species as
discussed i
Hi Popko,
My sense is that if the polytomy is hard, it is never necessary to
subtract a degree of freedom. If the polytomy is "firm" (sensu Purvis &
Garland 1993) - in that the true tree is fully bifurcating but we cannot
resolve a multifurcating node due primarily to rapid divergence of the
Hello,
Is clustal multiple sequence alignment implemented in any R packages, or is
there an easy way to call ClustalW on your hard drive from R, perhaps with
system()
Sincerely,
Scott Chamberlain
Rice University, EEB Dept.
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Dear all,
Can somebody tell whether one should subtract degrees of freedom when
applying PGLS with a phylogeny containing soft polytomies? And does it make
a difference if polytomies originate from data from multiple specimens of
species?
cheers, Popko Wiersma
- I reposted this message beca
