date:20161216

Re: [R-sig-phylo] Comparing support values on different trees

2016-12-16 Thread Emmanuel Paradis


Hi Frank,

It seems that you can use the (apparently not used a lot) option from 
makeNodeLabel(, method = "md5sum") which creates node labels with the 
MD5SUM algorithm using the tip labels descending from each node 
(considering the tree as rooted). The result is, for each node, a label 
that is unique for a given set of tip labels (even among different trees).


Taking your 1st tree:

R> tr <- read.tree(text = "(A:0.1, (B:0.2, (C:0.3, D:0.4)100:0.5)95:0.55);")
R> BP <- tr$node.label
R> trbis <- makeNodeLabel(tr, "md5sum")
R> names(BP) <- trbis$node.label

BP is a vector which you can index with labels built in the same way 
from another tree.


Cheers,

Emmanuel

PS: if the labelled topologies are identical for all trees as in your 
example below, then the node labels will be ordered in the same way in 
all trees and the above procedure is not needed.


Le 16/12/2016 à 17:57, Frank T Burbrink a écrit :

Hi Everyone,

Thank you Jacob, Keith and Emmanuel for your responses. What I am trying to do 
is a little different than what the solutions posted here would do. I am not 
important a distribution of trees, but rather a single tree with the support 
values already included. So imagine something like comparing support for three 
trees (the first two are bootstraps is from bootstraps, the third is Pp):

  1.  (A:0.1, (B:0.2, (C:0.3, D:0.4)100:0.5)95:0.55);
  2.  (A:0.1, (B:0.2, (C:0.3, D:0.4)60:0.5)20:0.55);
  3.  (A:0.1, (B:0.2, (C:0.3, D:0.4)1:0.5)0.8:0.55);

This would show that support for clade BCD would be 95, 20, 0.8 in each of the 
three trees and support for CD would 100, 60 and 1.0 respectively.

Is there a method that could read the trees with support, find the shared 
clades, and generate a table by node for all three support values?


Thanks!

Frank

Frank T. Burbrink, Ph.D.
Associate Curator
Department of Herpetology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192

fburbr...@amnh.org

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Re: [R-sig-phylo] ape chronos error

2016-12-16 Thread Emmanuel Paradis


Hi Riana,

It's difficult to answer your question.

Can you send some sample data to reproduce this error?

Best,

Emmanuel

Le 15/12/2016 à 22:58, Riana Rishad Minocher a écrit :

Hi,

I’m writing with an issue using the chronos function in ape:

I have a rooted supertree of 186 taxa (genetic & linguistic data), and am trying to 
time-calibrate with a set of divergence dates (genetic & linguistic; available for 
about 1/3 of nodes).

I’m using chronos and calling agemin and agemax from a table of dates:

tree.dated <- chronos(tree, calibration = makeChronosCalib(tree, node=dat$node, 
age.min=dat$agemin, age.max=dat$agemax))

I have the following error:

Setting initial dates...
Fitting in progress... get a first set of estimates

Error in nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) :
  gradient function must return a numeric vector of length 161
In addition: Warning message:
In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) :
  NA/NaN function evaluation

I have had a brief look at the chronos function, and cannot determine where the 
error is generated. The error message is slightly different if I alter the 
substitution model, and seems to trip up at a different point. I’m not sure if 
it begins in setting “ini.rate” as this appears to be where the error appears 
for model = “discrete”.

I have tried updating ape, altering my set of dates to a few nodes, removing 
the date for the root, listing node numbers and ages rather than calling it 
from the table, and reading my tree with read.nexus and in parenthetic format 
in case the tree object was problematic. I’ve noticed that the vector length 
the gradient function must generate varies depending on the number of known 
node ages provided - but I can’t figure out much more than that.

I was hoping someone had some suggestion on how I can deal with this error - 
essentially where the source of the error might be so I can adjust my input 
accordingly! Or, alternatively if anyone has a suggestion for different ways to 
time-calibrate the tree (other than chronos).

Thank you!

Best,

Riana

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Re: [R-sig-phylo] Comparing support values on different trees

2016-12-16 Thread Frank T Burbrink

Hi Everyone,

Thank you Jacob, Keith and Emmanuel for your responses. What I am trying to do 
is a little different than what the solutions posted here would do. I am not 
important a distribution of trees, but rather a single tree with the support 
values already included. So imagine something like comparing support for three 
trees (the first two are bootstraps is from bootstraps, the third is Pp):

  1.  (A:0.1, (B:0.2, (C:0.3, D:0.4)100:0.5)95:0.55);
  2.  (A:0.1, (B:0.2, (C:0.3, D:0.4)60:0.5)20:0.55);
  3.  (A:0.1, (B:0.2, (C:0.3, D:0.4)1:0.5)0.8:0.55);

This would show that support for clade BCD would be 95, 20, 0.8 in each of the 
three trees and support for CD would 100, 60 and 1.0 respectively.

Is there a method that could read the trees with support, find the shared 
clades, and generate a table by node for all three support values?


Thanks!

Frank

Frank T. Burbrink, Ph.D.
Associate Curator
Department of Herpetology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192

fburbr...@amnh.org

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Re: [R-sig-phylo] bonferroni corrections in Blomberg's K and Pagel's lambda

2016-12-16 Thread Chen, Ting-Wen

Hi Carmelo,

thank you so much for the suggestions. =)

All the best
Ting-Wen


--
Ting-Wen Chen
J.F. Blumenbach Institute of Zoology and Anthropology
Georg August University Goettingen
Berliner Str. 28
D-37073 Goettingen, Germany
Tel: +49-55139-10943

r-sig-phylo-requ...@r-project.org 於 
2016年12月16日 19:00 寫道：

Message: 5
Date: Fri, 16 Dec 2016 05:02:23 +0100
From: Carmelo Fruciano >
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] bonferroni corrections in Blomberg's K and
Pagel's lambda
Message-ID: 
<20161216050223.47442dfb1b3g9...@webmail.unict.it>
Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed"

Hi Ting-Wen,
as Ted pointed out, if and how one has to correct for multiple tests
is a huge topic. Perhaps looking at the literature and making your own
opinion on this matter would be the best choice (for example, Perneger
1998 - British Medical Journal and Garcia 2004 - Oikos, present two
different points of view in a very accessible way).

A few extra points:
- There are other methods that are generally less conservative than
the Holm procedure ("Sequential Bonferroni"); these include the
Benjamini-Hochberg procedure (Benjamini & Hochberg 1995 - Journal of
the Royal Statistical Society; see also Benjamini & Yekutieli 2001 -
The Annals of Statistics) and other more recent procedures (such as
Carvajal-Rodriguez & de Una-Alvarez 2011 - Plos One); most of these
are worth checking out, making your opinion on them and, possibly,
using them (most of them have R implementations)

- If your dataset is multidimensional/multivariate in nature, you
might want to consider using multivariate approaches for estimating
and testing for phylogenetic signal (e.g., Adams 2014 - Systematic
Biology), rather than many univariate tests

- If your dataset/hypothesis is multivariate in nature, testing
individual PCs separately might be a poor choice (especially for PCs
of order higher than 1), if it is not multivariate in nature, there
might be no reason to use PCA

I hope this is of some help.
Best,
Carmelo



--
Carmelo Fruciano
Postdoctoral Fellow - Queensland University of Technology - Brisbane,
Australia
Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/


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Re: [R-sig-phylo] Comparing support values on different trees

Re: [R-sig-phylo] ape chronos error

Re: [R-sig-phylo] Comparing support values on different trees

Re: [R-sig-phylo] bonferroni corrections in Blomberg's K and Pagel's lambda

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