[Phylobase-devl] conversion from ade4 to phylog format: problem

[Jombart, Thibaut]

Dear Peter, 

the phylog class in ade4 is now deprecated. The package adephylo replaces and extends the phylogeny-related methods in ade4 (and uses phylo, phylo4, and phylo4d objects).
You'll find more information about it in a small application note: 
http://bioinformatics.oxfordjournals.org/content/26/15/1907.abstract

The package is available on CRAN for the stable version, and on R-forge for the devel.

Best regards

Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: phylobase-devl-bounces at lists.r-forge.r-project.org [phylobase-devl-bounces at lists.r-forge.r-project.org] On Behalf Of Peter B. Pearman [pearman at wsl.ch]
Sent: 25 October 2010 13:14
To: phylobase-devl at lists.r-forge.r-project.org
Subject: [Phylobase-devl] conversion from ade4 to phylog format: problem

Hello phylobase users and developers,

I've got a little problem that seems strange.  Perhaps one of you can
enlighten me?

It seems that with updating to R-version 2.12.0 (2010-10-15) the
following code no longer works:

 >  tree <-
drop.tip(tree,name.check(tree,data.names=names.final)$Tree.not.data)
 > tree$node.label <- paste("node_",as.character(c(410:807)),sep="")
 > phylo4.tree <- as(tree,"phylo4")
 > tree.phylog <- as(phylo4.tree,"phylog")
There were 50 or more warnings (use warnings() to see the first 50)

 > warnings()
Warning messages:
1: In STRING[k] <<- x :
   number of items to replace is not a multiple of replacement length
2: In STRING[k] <<- x :
   number of items to replace is not a multiple of replacement length

(continues ad nauseum)

The node names are all mixed up and there seem to be other problems as well:

 > tree.phylog$nodes
     node_410   node_410_1   node_410_2   node_410_3   node_410_4
node_410_5
    16.252392     8.929608    24.678913     9.461009     5.245589
32.854018
   node_410_6   node_410_7   node_410_8   node_410_9  node_410_10
node_410_11
    17.960096    15.064738    21.827794     2.024337    49.192003
42.923378
  node_410_12  node_410_13  node_410_14  node_410_15  node_410_16
node_410_17

I re-installed phylobase from source on my MacOS (snow-L 10.6.4), but
that did not fix the problem.  All phylogenetics and statistical
packages have been updated.

My office mate ran the same code on his Mac, with R-version:
2.11.1 (2010-5-31)
and a previous binary installation of phylobase.  Everything worked fine
for him.

I can supply the relevant objects if someone needs to try this on your
machine.

Any help greatly appreciated.

Best,

Peter


--
Peter B. Pearman


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