[R-sig-phylo] Rooting on a node with resolve.root = TRUE
Dear phylofolks,
I'm trying to root a tree on an internal (rather than a terminal) branch.
Here is a small example:
library(ape)
t5 - rmtree(N = 1, n = 5, rooted = FALSE)[[1]]
root(t5, node = 6, resolve.root = TRUE)
output: Error in if (i != N) { : argument is of length zero
root(t5, node = 7, resolve.root = TRUE)
output: Phylogenetic tree with 5 tips and 4 internal nodes.
Tip labels:
[1] t4 t3 t2 t5 t1
Rooted; includes branch lengths.
I don't understand why rooting at node 6 throws an error, while using node
7 is fine. What am I missing?
Cheers,
Luiz
--
Luiz Max Fagundes de Carvalho
PhD student, Institute of Evolutionary Biology, School of Biological
Sciences,
Ashworth Laboratories, Ash 2, office 123
University of Edinburgh, United Kingdom.
http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283
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[R-sig-phylo] Count the number of character/state changes in a tree
Dear Phylofolks,
Suppose I have a phylo object phy and the states at all nodes (internal and
external). Would the following function give me the number of state changes?
get.changes - function(tree, states){
sum(apply(phy$edge, 1, function(x) states[x[1]]!=states[x[2]]))
}
If not, what would?
Thanks in advance,
Luiz
--
Luiz Max Fagundes de Carvalho
PhD student, Institute of Evolutionary Biology, School of Biological
Sciences,
Ashworth Laboratories, Ash 2, office 123
University of Edinburgh, United Kingdom.
http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283
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[R-sig-phylo] Potential glitch in phymltest
Hello Phylofolks,
I've been using ape::phymltest() for a while now on a project and I just
realised there is a potential glitch in the function. The reason is that
the order of the models in the 'mdl' object inside the function is
different from the order in .phymltest.model, what causes the cmd object to
mess up.
The following MWE should do the job of showing my point:
### begin MWE
library(ape)
.phymltest.model -
c(JC69, JC69+I, JC69+G, JC69+I+G,
K80, K80+I, K80+G, K80+I+G,
F81, F81+I, F81+G, F81+I+G,
F84, F84+I, F84+G, F84+I+G,
HKY85, HKY85+I, HKY85+G, HKY85+I+G,
TN93, TN93+I, TN93+G, TN93+I+G,
GTR, GTR+I, GTR+G, GTR+I+G)
phymltest.test - function(seqfile, format = interleaved, itree = NULL,
exclude = NULL, execname = NULL, append = TRUE)
{
N - length(.phymltest.model)
format - match.arg(format, c(interleaved, sequential))
fmt - rep(, N)
if (format != interleaved) fmt[] - -q
boot - rep(-b 0, N) # to avoid any testing
mdl - paste(-m, rep(c(JC69, K80, F81,HKY85,F84, TN93,
GTR), each = 4))
tstv - rep(-t e, N) # ignored by PhyML with JC69 or F81
inv - rep(c(, -v e), length.out = N)
## no need to use the -c option of PhyML (4 categories by default if '-a
e' is set):
alpha - rep(rep(c(-c 1, -a e), each = 2), length.out = N)
tree - rep(, N)
cmd - paste(execname, -i, seqfile, fmt, boot, mdl, tstv, inv, alpha,
tree, --append )
imod - 1:N
if (!is.null(exclude)) imod - imod[!.phymltest.model %in% exclude]
for (i in imod) print(cmd[i])
}
phymltest.test(seqfile = seqname,
exclude = c(K80, K80+I, K80+G, K80+I+G,
F81, F81+I, F81+G, F81+I+G,
F84, F84+I, F84+G, F84+I+G,
TN93, TN93+I, TN93+G, TN93+I+G),
execname = execname)
1] execname -i seqname -b 0 -m JC69 -t e -c 1 --append
[1] execname -i seqname -b 0 -m JC69 -t e -v e -c 1 --append
[1] execname -i seqname -b 0 -m JC69 -t e -a e --append
[1] execname -i seqname -b 0 -m JC69 -t e -v e -a e --append
[1] execname -i seqname -b 0 -m F84 -t e -c 1 --append
[1] execname -i seqname -b 0 -m F84 -t e -v e -c 1 --append
[1] execname -i seqname -b 0 -m F84 -t e -a e --append
[1] execname -i seqname -b 0 -m F84 -t e -v e -a e --append
[1] execname -i seqname -b 0 -m GTR -t e -c 1 --append
[1] execname -i seqname -b 0 -m GTR -t e -v e -c 1 --append
[1] execname -i seqname -b 0 -m GTR -t e -a e --append
[1] execname -i seqname -b 0 -m GTR -t e -v e -a e --append
## end MWE
I think it's easily solved by replacing mdl with paste(-m, rep(c(JC69,
K80, F81, F84HKY85, TN93, GTR), each = 4))
Anyways, hope to clarify this minor issue.
Cheers,
Luiz
--
Luiz Max Fagundes de Carvalho
PhD student, Institute of Evolutionary Biology, School of Biological
Sciences,
Ashworth Laboratories, Ash 2, office 123
University of Edinburgh, United Kingdom.
http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283
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Re: [R-sig-phylo] Sampling bias in discrete trait estimation
This definitely looks like something. Thanks, Matt! Cheers, Luiz 2013/11/11 Matt Pennell mwpenn...@gmail.com Hi Luiz, Yes, non-random sampling of traits, if not taken into account will certainly bias the estimation of the transition parameters. Methods for addressing this have been developed by Rich FitzJohn and colleagues http://sysbio.oxfordjournals.org/content/58/6/595.short (this was discussed in the context of state dependent diversification but also applies to regular Mk models, which is just a special case of the BiSSE model). I am sure there are potentially interesting follow-ups one could do here. cheers, matt On Mon, Nov 11, 2013 at 9:52 AM, Luiz Max Carvalho luizepidemiolo...@gmail.com wrote: Dear all, Suppose you have observed K discrete traits for a phylogeny with N tips. For some reason, you think your trait sampling is not random, i.e., it may be biased towards some particular K's, for example because they're easier to sample. I imagine this will introduce some bias in the estimation of the infinitesimal rate matrix of the Markov model of trait evolution (Q). I would like to address this question in a more mathematically precise way. Have anyone heard of a study addressing these issues so far, both mathematically or using simulation studies? Thanks in advance. All the best, Luiz -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[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/ -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[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] Does anyone know about a function to remove redundancy from a database?
I've been looking for a function that could scan a DNAbin object and return just the unique sequences. Does anyone know about a function for that? Thanks in advance, -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[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/
Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?
Great! Thank you! 2013/2/19 Klaus Schliep klaus.schl...@gmail.com Hi Luiz, phangorn has a generic unique function for phyDat objects. There may be more elegant ways, but this code should work: library(phangorn) y = as.DNAbin(unique(as.phyDat(x))) Cheers, Klaus On 2/19/13, Luiz Max Carvalho luizepidemiolo...@gmail.com wrote: I've been looking for a function that could scan a DNAbin object and return just the unique sequences. Does anyone know about a function for that? Thanks in advance, -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[alternative HTML version deleted]] -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[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/
