am
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> On 1/31/2019 12:48 PM, Roland Sookias wrote:
> > De
Dear all,
I want to get squared change parsimony ancestral state reconstructions for
a matrix into R.
I have tried the asr_max_parsimony() function from castor, but the results
are not the same as in Mesquite for example. To take an example, a
two-taxon clade with a unique state for these taxa op
y that a particular curve in the dorsal margin of the ilium
in crocodile-line crocodilians is homologous, but I don't want to
hypothesize homology of those taxa "lacking" this state. They are all
equally far from each other.
Thanks very much indeed
Best
Roland Sookias
> Best
> Luke
>
> -Original Message-
> From: Alejandro Gonzalez Voyer [mailto:alejandro.gonza...@ebd.csic.es]
> Sent: Wednesday, September 12, 2012 2:23 AM
> To: Roland Sookias
> Cc: Luke Matthews; r-sig-phylo@r-project.org
> Subject: Re: [R-sig-phylo] MRM(), AI
; r-sig-phylo-requ...@r-project.org
>
> You can reach the person managing the list at
> r-sig-phylo-ow...@r-project.org
>
> When replying, please edit your Subject line so it is more specific than "Re:
> Contents of R-sig-phylo digest..."
>
>
&g
Dear all,
I am trying to find a way of quantifying the relative effects of
linguistic phylogeny, geography, and other cultural influences, namely
religion and communism, on "trait" values for countries (e.g. GDP).
I am currently thinking that carrying out a regression on distance
matrices (i.e. e
Hi
Can anyone help me interpret the output from phytools' rate.evol.mcmc
function? I get, as it says I should, "results from the MCMC run" and
a "tips list of stips in state sig(1)^2 for each sampled generation of
MCMC (to polarize the rate shift).", but I'm not sure what I'm looking
for practical
ages, rlen = 10, method = "equal")
On Thu, Jul 21, 2011 at 5:12 PM, Klaus Schliep wrote:
> Hi Roland!
> ages should be a matrix, with row names and the ages in the first column.
>
> On 7/21/11, Roland Sookias wrote:
>> Great! It worked. What format should the f
Cheers, yes I retrieved it and it worked!
On Thu, Jul 28, 2011 at 1:16 AM, Jonathan Eastman
wrote:
> Hi Roland,
>
> You might have better luck installing the precompiled version for Windows
> (auteur_0.11.0612.zip), which can be retrieved from
> http://cran.r-project.org/web/packages/auteur/index
Hi
Can anyone tell me what the "a" parameter in the EB model in geiger is?
Thanks
Roland
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Looks like a windows zip and mac bin are now available - solved all my
problems! :)
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Hi
I'm trying to install auteur on R 2.13.1 on windows. With the archive
I get an error (below). Can anyoen help?
> utils:::menuInstallLocal()
Error in gzfile(file, "r") : cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
documentation, for which I am grateful to you! It should read
> 'nchar*(nchar+1)/2'. In your case, you must supply a scalar value, a guess
> as
> to what the square root of alpha should be.
>
> I will repair the documentation and upload a new version of ouch to CRAN
y that this is
> indeed the only problem.
>
> Regarding the initialization of the hansen optimizer (sqrt.alpha, sigma), I
> assume you have read '?hansen'. Can you be more specific as to what is not
> clear to you?
>
> On Monday, July 25, 2011 08:53:12 AM Roland S
Hi
I posted this on r-help by accident, and realize it's more appropriate here,
so I'll send it here and do ignore the other post.
I'm trying to use ouch's hansen and brown functions but I get the error:
> brown(logflatnodes,archotreeouch)
Error in backsolve(l, x, k = k, upper.tri = upper.tri, t
ng to do with ape).
> Try this:
>
> tmp = read.csv("agescut.csv", header=FALSE)
> ages = matrix(tmp[, 2], ncol=1)
> rownames(ages) = tmp[,1]
> tree = read.tree("archotreeresolved6.tre")
> ttree<-date.phylo(tree, ages, rlen=1, method="equal")
&
be good if you add the datasets, that one can reproduce your
> results (archotreeresolved, ages). I would guess from the error
> message that your ages list may has the wrong format.
> Also traceback() sometimes tells you where the error happens exactly.
>
> Kind regards
> Klaus
Hi all
I'm trying to assign lengths to branches in a tree using the Ruta et al.
2008 method via Graeme Lloyd's date.phylo() function (see
http://www.graemetlloyd.com/methdpf.html). I keep coming up against an error
for some reason. Graeme himself does exactly the same thing seemingly on his
Mac (I
Hi
I keep getting an error like this:
Error in `coef<-.corARMA`(`*tmp*`, value = c(18.3113452983211,
-1.56626248550284, :
Coefficient matrix not invertible
or like this:
Error in gls(archlogfl ~ co2, correlation = corARMA(p = 3)) : false
convergence (8)
with the gls function in nlme.
The f
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