1,i]));
# apply it. this assume you want to extend it, not just set it
phy$edge.length[idx] <- phy$edge.length[idx] + as.numeric(df[i,2]);
}
Probably a nicer way to do it without a loop...
JWB
____
Joseph W. Brown
Post-doctoral Researcher,
If you want to just extend all tips by a constant amount you can do this:
# extend terminal edges by arbitrary amount (here: 13)
idx <- which(phy$edge[,2] < (phy$Nnode + 1));
phy$edge.length[idx] <- phy$edge.length[idx] + 13;
HTH.
Joseph.
____
Joseph
ncestor
>> for (i in 2:length(tnd)) {
>> done <- FALSE;
>> cnd <- tnd[i];
>> while (!done) {
>> cpar <- pvec[cnd]; # get immediate parent
>> if (cpar %in% pars) {
>> if (cpar
Sweet! I considered preallocation, but figured it was not worth it. Guess I was
wrong!
JWB
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Scie
for my purposes.
JWB
____
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
> On 9 Jun, 2017, a
w00t!
I am aware that `which` is inefficient, but wasn't sure how to get around it in
this instance. Thanks!
It would be great to have this in the new version!
Joseph.
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
# keep going!
cnd <- cpar;
}
}
}
return(pars[mrcaind]);
}
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences
HTH.
JWB
____
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
> On 17 May, 2017, at 08:12, Fábio Machado <macfa.
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
> On 8 May, 2017, at 07:31, David Buckley <dbuck...@mn
de 10 (node 27) has 2 tips."
[1] "clade 11 (node 28) has 2 tips."
[1] "clade 12 (node 29) has 6 tips."
[1] "clade 13 (node 30) has 2 tips."
[1] "clade 14 (node 31) has 4 tips."
[1] "clade 15 (node 32) has 3 tips."
[1] "clade 16 (node 33)
ething
}
This includes the root node (i.e. whole tree), but that can be changed. This
can be rewritten as an lapply if necessary.
HTH.
JWB
____
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutiona
I wonder if reading in a Nexus file with a translation table bypasses this
problem?
JWB
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Scie
Here is a cheeky post <http://opensoul.org/2015/07/22/99ways/> by Brandon
Keepers on how to do things wrong when developing open source software. Lots of
good stuff in there!
JWB
____
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
Univ
how sites/partitions are ordered).
If you need these in out another format (say, phylip), do:
./pxcat -s *.fas -o my_concatenated_alignment.fas | ./pxs2phy -o
my_concatenated_alignment.phy
HTH.
JWB
________
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
://floating-point-gui.de
Comparing Floating Point Numbers, 2012 Edition:
https://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
HTH.
JWB
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
> On 16 Aug, 2016, at 10:15, Klaus Schliep <klaus.schl...@gmail.
am and the results are
the same. So can we assume this is not a PhyloBayes issue, and rather an
unavoidable problem with large, old trees? But the fact that MrBayes trees are
ultrametric is confusing; does MrBayes use less precise edge lengths?
JWB
____________
Jo
.
3. If all else fails, and it is not too much trouble, use a virtual box, and
install/use treePL in some flavour of linux. This should work flawlessly.
HTH.
JWB.
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department
://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
_
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology Evolutionary Biology
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