[R-sig-phylo] Problems with dependency Biostrings
Hello all,
there have been a few reports of problems with installing phytools or
phangorn and you may see something like this:
devtools::install_github("liamrevell/phytools")
Downloading GitHub repo liamrevell/phytools@master
Installing phytools
Skipping 1 packages not available: Biostrings
...
...
Error: Command failed (1)
Recently I updated phangorn (now version 2.0.1), but there were also
updates of R (3.2.3) and also Bioconductor. All this seem to have
contributed to this problem. install.packages() and install.github() do not
always get bioconductor dependencies right (e.g.
https://github.com/hadley/devtools/issues/700).
To solve the problem simply install the Biostrings package first
source("http://bioconductor.org/biocLite.R;)
biocLite("Biostrings")
and in a fresh session of R try again to install phytools or phangorn.
If you have installed any bioconductor packages, chances are that you also
installed Biostrings package are pretty high.
Regards,
Klaus
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
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[R-sig-phylo] interpreting PGLS results when lambda>1
Hi everyone, I have been running PGLS with gls from NLME and phyl.resid from PHYTOOLS. Most of my analyses are running well with no problems and give the same results in both packages. With just a few of my dependent variables, which happen to be evolutionary rates extracted from the program BAMM and the associated package BAMMtools, I get lambda values greater than 1 when using both gls and phyl.resid. I have read an older post that says that lambda can theoretically be >1, but I am wondering whether it is safe to interpret results from such PGLS analyses? If I constrain lambda to be 1 (instead of 1.0015, which gls and phyl.resid return when letting them optimize lambda) the results and p-values change considerably. Any advice or experience with how to proceed or interpret results in light of lambda greater than 1 would be greatly appreciated! Thanks for your time! Regards, Zach [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Detecting homoplasy
Hi all,
I am interested in finding homoplasious sites in a nucleotide sequence
alignment on a ML tree calculated from that alignment. Is there a commonly
used approach for doing this in ape, phangorn etc. I have tried a number of
google searches based around 'R homoplasy' but cant find anything.
On a related note, is there a function available to calculate the consistency
index for a given position on an alignment rather than an average for the whole
alignment, which is what CI in phangorn does now?
thanks!
Tim
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