gmane.comp.lang.r.phylo

Re: length of attribute (names) when calculating independent contrasts

Agus Camacho — 2012-05-25T17:29:47

Thanks emmanuel,

Got this:

 tree$node.label [1]  1  2  3  4  5  6  7  8  9 10> tree$Nnode[1] 9


Wonder how is that possible. So im sending how i generated the tree.
tree <- read.tree(text="
((((C.leiolepis:0.0168, C.nicterus:0.0099):0.0242
,C.sinebrachiatus:0.024):0.074
,(S.catimbau:0.0652,N.ablephara:0.0309):0.0648):0.0659

,((((P.erythrocercus:0.0235,P.tetradactylus:0.0259):0.0462
,V.rubricauda:0.124):0.0225
,M.maximiliani:0.0615):0.0828
,P.paeminosus:0.1093):0.0131);")

tree$node.label=c(1,2,3,4,5,6,7,8,9,10)
plot(tree,show.node.label=TRUE,use.edge.length=TRUE)


2012/5/24 Emmanuel Paradis <Emmanuel.Paradis-ysPYPCwjBSM< at >public.gmane.org>

Re: length of attribute (names) when calculatingindependent contrasts

Emmanuel Paradis — 2012-05-25T02:33:04

Hi Agus,

It seems the problem comes when pic() tries to create names to the 
contrasts. Probably your tree has badly formatted node labels. What do 
the following commands return?

tree$node.label
tree$Nnode

Cheers,

Emmanuel

Agus Camacho wrote on 25/05/2012 01:58:

length of attribute (names) when calculatingindependent contrasts

Agus Camacho — 2012-05-24T18:58:05

Hi all,

When calculating independent contrasts of a variable, I get the following
message:

  el atributo 'names' [10] debe tener la misma longitud que el vector [9]
The attribute "names" [10] must have the same length than the vector[9]
(this was translated by me)

After checking the help on the command, i made the following

observations,
 > length(Weight)[1] 10> class(Weight)[1] "numeric"> tree$tip.label
[1] "C.leiolepis"      "C.nicterus"       "C.sinebrachiatus"
 [4] "S.catimbau"       "N.ablephara"      "P.erythrocercus"
 [7] "P.tetradactylus"  "V.rubricauda"     "M.maximiliani"
[10] "P.paeminosus"    > class(tree)[1] "phylo"

       0.9020000        0.7155556        0.5370526        0.5887500
     N.ablephara  P.erythrocercus  P.tetradactylus     V.rubricauda
       0.5460000        0.4127273        0.3970000        0.4725294
   M.maximiliani     P.paeminosus
       0.4833333        0.4677692



However, to me, everything seems to be right about the names and the
vector's length. Any hint?

Thanks to

Re: problem with fitcontinuos function

Agus Camacho — 2012-05-23T20:32:14

Thanks to all for your fast answer, this list is amazing!

Graham's answer was perfectly satisfactory, once onnly that eliminated the
warning.

Thanks to all again.
Agus

2012/5/23 Graham Slater <gslater-xwz7R8GQi1g< at >public.gmane.org>

Re: problem with fitcontinuos function

Renata Brandt — 2012-05-23T20:27:24

Hello Agus,

I believe your problem will be solved if you set row names to the object
tp$temperature.

An example follows:
names(temperature)<-row.names(tp)

Please let me know if it worked.
Cheers, Renata

Re: problem with fitcontinuos function

Luke Harmon — 2012-05-23T20:23:32

Hi Agus - 

This might be a problem with node labels - try trimming them off of the tree and see if it works.

tree$node.label<-NULL


On May 23, 2012, at 1:16 PM, Agus Camacho wrote:


Luke Harmon
Assistant Professor
Biological Sciences
University of Idaho
208-885-0346
lukeh-Meo6Lv8EUjg3uPMLIKxrzw< at >public.gmane.org

problem with fitcontinuos function

Agus Camacho — 2012-05-23T20:16:54

Dear all,

fitcontinuous is giving me a warning generally related to non
correspondence between tree tips and data. However name.check and the tree
tips seems ok.

Anybody has a hint on this?

Thanks in advance.
Agus

Fitting  BM model:> tree
Phylogenetic tree with 11 tips and 10 internal nodes.

Tip labels:
C.leiolepis, C.nicterus, C.sinebrachiatus, S.catimbau, N.ablephara,
P.erythrocercus, ...
Node labels:
1, 2, 3, 4, 5, 6, ...

Rooted; includes branch lengths.

General question about the impact of sampling bias incomparative and diversification analyses

Julien Lorion — 2012-05-23T17:14:21

Dear all,

I have a 5-gene phylogenetic tree, dated, quite well resolved, including 50 species and covering 80~90% of the known diversity... I have also LASER diversification analyses and bayesian reconstruction of ancestral states for 5 characters , both taking into account the impact of sampling biases...

I evaluate now the adaptive significance of 5 characters  with ape/caper (using Pagel's test, GEE and pGLS) AND their impact of diversification (using the Yule model with covariates). My results makes perfectly sense in terms of biology but I am worrying about their their relevance.  Indeed, for 2 of my characters, I have only 50% of data... In another hand, the distribution of data is well balanced among lineages... and I would say that corresponding patterns of evolution inferred from Bayesian analyses are pretty clear... 

I now the Beast team is working on an implementation of a Bayesian model for correlation analysis, that takes into account uncertainties (and thus missing data). But it is not ready

Re: PIC or PGLS for genome-wide SNP screening

Anthony R Ives — 2012-05-23T15:45:04

Ted and Mattia,

For comparisons among models with the same parameters (such as OLS  
vs. PGLS), check out:

Vuong, Q. H. 1989. Likelihood ratio tests for model selection and non- 
nested hypotheses. Econometrica 57:307-333.
Clarke, K. A. 2007. A simple distribution-free test for nonnested  
model selection. Political Analysis 15:347-363.

I haven't tried these tests in this context, but they might be  
appropriate.

Cheers, Tony


On May 23, 2012, at 10:30 AM, Theodore Garland Jr wrote:


Anthony Ragnar Ives
Department of Zoology
UW-Madison
(608) 262-1519


[[alternative HTML version deleted]]

Re: PIC or PGLS for genome-wide SNP screening

Theodore Garland Jr — 2012-05-23T15:30:40

If you have the same set of independent variables, then you just prefer the one (OLS or PGLS) with the higher likelihood.  So far as I am told by Joe Felsenstein, you cannot do a ln maximum likelihood ratio test because the number of parameters is the same, although this paper seems to suggest otherwise:
Mooers, A. O., S. M. Vamosi, and D. Schluter. 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in cranes (Gruinae). American Naturalist 154:249-259.

For two models with the same set of independent variables, AIC does not add anything for you.

If you go to something like Regression with an OU process modeled for the residuals, then you do have an additional parameter being estimated and so you can do an ln maximum likelihood ratio test of that model versus OLS and versus PGLS.  For example, see:
Lavin, S. R., W. H. Karasov, A. R. Ives, K. M. Middleton, and T. Garland, Jr. 2008. Morphometrics of the avian small intestine, compared with non-flying mammals: A phylogenetic perspe

PIC or PGLS for genome-wide SNP screening

Mattia Prosperi — 2012-05-23T15:05:31

Dear all,

I am working on a data set composed of bacterial genomic sequences (a
few genes) associated to phenotypic values (in-vitro resistance to
antibiotics, a numerical value discretised into a binary class). Of
note, the bacterial isolates were sampled non-uniformly at different
times and locations, thus with a possible sampling bias. The data set
is ~1,000 variables and ~1,000 observations.

I have been applying several methods for developing a model to predict
antibiotic resistance from the single nucleotide polymorphisms (SNP)
extracted from a multiple alignment, applying classical statistical
learning and feature selection methods.
Eventually, I found that a logistic regression with main effects,
where the variables were selected first by a univariable chi-square
screening and then by AIC stepwise, was as good as other more complex
and non-linear methods (such as random forests) by comparing different
loss function (AUROC, specificity, sensitivity) distributions  upon
multiple cross-validation runs.

Zero value of a significant model parameter duringPGLS

Agus Camacho — 2012-05-23T01:54:25

Dear all,

I just had the following result fitting a Pgls with both, brownian and O-U
correlation structures.
I was wandering what could have made the value and Sd go to zero. Altitude
values were considered continuous but were strongly grouped in two levels.
Might that have to do with the result?

Would appreciate any hint.
There goes the model's summary.
Thanks in advance.


Generalized least squares fit by maximum likelihood
  Model: temperature ~ 1 + altitude
  Data: tp
  AIC BIC logLik
   60  62    -26

Correlation Structure: corMartins
 Formula: ~1
 Parameter estimate(s):
alpha
   21

Coefficients:
            Value Std.Error t-value p-value
(Intercept)    35       2.8    12.7   0.000
altitude        0       0.0    -2.2   0.057

 Correlation:
         (Intr)
altitude -0.93

Standardized residuals:
   Min     Q1    Med     Q3    Max
-1.907 -0.519  0.034  0.734  1.859

Residual standard error: 2.7
Degrees of freedom: 11 total; 9 residual

Re: center of tree

Klaus Schliep — 2012-05-22T10:28:46

Hello Mathias,

I'm not aware of any general  COT in R, your chance to make a contribution.
Midpoint rooting is the COT for a special function F [2], it minimizes
the maximum
distance from the root (COT) to the tips.

Cheers,
Klaus



On 5/18/12, Walter, Mathias <mathias-taBouHiV1h1goHlPtYpdqQ< at >public.gmane.org> wrote:

compute HKY85 distances in R

Juan Antonio Balbuena — 2012-05-22T09:49:55

Hello
I would like to know whether it is possible to compute HKY85 genetic
distances using R. The model is not included in the dist.dna function
of ape and I was wondering whether it is available in another package.
Thank you very much for your attention.

Juan Antonio Balbuena

Re: unrooted tree, spread tips

Emmanuel Paradis — 2012-05-18T11:34:39

Walter, Mathias wrote on 18/05/2012 18:16:

This should not happen. May be a bug. You have an example of this?

E.

Re: unrooted tree, spread tips

Walter, Mathias — 2012-05-18T11:16:34

Hi,

if I use type="r", then quite a lot of lines cross. I tried optimal
tree ordering but as soon as I convert my hclust object to a phylo
object (via as.phylo), the ordering is lost.

Another advantage of the unrooted tree is, that you can often clearly
distinguish main clusters. That is not possible with any other kind of
tree drawing.

--
Kind regards,
Mathias

2012/5/18 Emmanuel Paradis <Emmanuel.Paradis-ysPYPCwjBSM< at >public.gmane.org>:

Re: unrooted tree, spread tips

Emmanuel Paradis — 2012-05-18T10:53:13

Hi,

Walter, Mathias wrote on 18/05/2012 16:42:

No. The only available algorithm for unrooted trees in ape is the 
"equal-angle" one. It seems that for your purpose type="r" might be not 
bad, even though the center of the circle is the root.

Best,

Emmanuel

unrooted tree, spread tips

Walter, Mathias — 2012-05-18T09:42:43

Hi,

I use ape to plot my phylogenetic trees. Often I have to plot unrooted
trees with few clades, but a lot of tips per clade. The tip labels are
hard to read, even if I use lab4ut="axial". Is there any way to spread
the tips? I saw this in some other tree drawing programs.

--
Kind regards,
Mathias

Re: Best way to test correlation between discrete andcontinuous variables ?

Patrik Lindenfors — 2012-05-17T10:04:19

Julien,
Regarding my paper, it was outdated already when published. Stick to the other suggestions given.

Best regards
                              - Patrik Lindenfors -

On 2012-05-17 11:51, Julien Lorion wrote:
 ne: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarland-3vSkeFsW7jA< at >public.gmane.org http://www.biology.ucr.edu/people/faculty/Garland.html Expe!
 rimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) ________________________________________ From: r-sig-phylo-bounces-0bNBQ1PAWB4BXFe83j6qeQ< at >public.gmane.org [r-sig-phylo-bounces-0bNBQ1PAWB4BXFe83j6qeQ< at >public.gmane.org] on behalf of Marguerite Butler [mbutler808-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org] Sent: Wednesday, May 16, 2012 12:27 PM To: Julien Lorion Cc: r-sig-phylo-0bNBQ

Re: Best way to test correlation between discrete andcontinuous variables ?

Julien Lorion — 2012-05-17T03:51:53

Alexandro, Marguerite and Ted...

Thanks a bunch for your valuable replies... 

Quickly after I sent my sos on the mailing list, I found Ted's paper and implementation of his method in Geiger... I also found the the Brunch algorithm (package Caper), a variation of the Felsenstein's PIC...

I'll add the GLS as Marguerite suggested...and it should be fine... 

I also found a paper by Lindenfors Patrick, introducing another type of phylogenetic ANOVA... But it looks like it has not been implemented yet in any software
http://zootis.zoologi.su.se/research/lindenfors/publications/Lindenfors_2006.pdf

Glad I have found this mailing list !! 

Regards

Julien






On May 17, 2012, at 5:58 AM, Theodore Garland Jr wrote:


Julien Lorion
PhD, Post-doctoral fellow of the Japan Society for the Promotion of Science
Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Marine Ecosystems Research Department
2-15 Natsushima, Yokosuka 237-0061 Japan
Phone: +81-46-867-9570, Fax: +81-46-867-9525

Re: Best way to test correlation between discreteandcontinuous variables ?

Theodore Garland Jr — 2012-05-16T20:58:25

Dear Julien,

I'll just add two other papers to your reading list (both available at my web page):

Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292.

And the Appendix of this paper:
Lavin, S. R., W. H. Karasov, A. R. Ives, K. M. Middleton, and T. Garland, Jr. 2008. Morphometrics of the avian small intestine, compared with non-flying mammals: A phylogenetic perspective. Physiological and Biochemical Zoology 81:526-550. [provides Matlab Regressionv2.m, released as part of the PHYSIG package]

Cheers,
Ted

Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone:  (951) 827-3524
Wet Lab Phone:  (951) 827-5724
Dry Lab Phone:  (951) 827-4026
Home Phone:  (951) 328-0820
Facsimile:  (951) 827-4286 = Dept. office (not confidential)
Email:  tgarland-3vSkeFsW7jA< at >public.gmane.org
http://www.biology.ucr.edu/people/faculty/Garland.html

Experime