Re: [R-sig-phylo] Possible Bug in ape::read.tree

Emmanuel Paradis Fri, 08 Sep 2017 06:33:19 -0700

Hi George,

Nice comparison! It would be interesting to see if the differencebetween ape and rncl is always in the same direction. It seems that thetrees in your test are all relatively small (timings are concentratedaround 1 ms). Apparently, read.tree scales a bit better thanread_newick_phylo with bigger trees:


R> write.tree(rtree(50000), file = "tr.tre")
R> system.time(a <- read.tree("tr.tre"))
utilisateur     système      écoulé
      0.240       0.004       0.245
R> system.time(b <- read_newick_phylo("tr.tre"))
utilisateur     système      écoulé
      0.380       0.020       0.397
R> identical(a, b)
[1] FALSE
R> all.equal(a, b)
[1] TRUE

Best,

Emmanuel

Le 07/09/2017 à 21:39, George Vega Yon a écrit :

Hi Klaus,

Since I'm actually working with the complete PANTHER 11.1 database, I wrote
a short document in our project's website comparing both ape and
rncl reading ~13,000 trees. ape::read.tree does the job and identifies and
reads the singleton as expected. Overall, while I see that the new version
of the read.tree function is significantly faster, it does not seem to be
significantly faster than rncl (both perform pretty good).

You can find the document here:
https://github.com/USCbiostats/aphylo/blob/master/playground/ape_now_supports_singletons.md

Best,



George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

On Tue, Sep 5, 2017 at 5:55 PM, Klaus Schliep <klaus.schl...@gmail.com>
wrote:

Dear George & list,
you can try install the development version of ape, which can handle
singleton nodes:
download.packages("ape", ".", repos = "http://ape-package.ird.fr/";)
and than install the package from source. See
http://ape-package.ird.fr/ape_installation.html for more details.
For you tree the new version seems to import tree fine.
Emmanuel and I are keen to get feedback on the new read.tree() function so
please give it a try.
Kind regards,
Klaus




On Tue, Sep 5, 2017 at 5:37 PM, Liam J. Revell <liam.rev...@umb.edu>
wrote:

Hi George. Mario is correct that phytools can read a tree with singleton
nodes (if that is indeed your problem), but the name of the function is
read.newick. Good luck! - Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org


On 9/5/2017 4:17 PM, George Vega Yon wrote:

Hi Mario,

That sounds great!

Thanks,

George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo <
mariojm...@gmail.com> wrote:

Hi, George,


Ape package do not read tree with singletons, yet. New version will
read.
You can use readTree from phytools package for while.

Best regards,

Mario


On 5 Sep 2017 5:53 p.m., "George Vega Yon" <g.vega...@gmail.com> wrote:

Hi,

When trying to read this tree with the ape::read.tree function :

((((((((((((((AN14:0.000,AN15:0.000):0.000[&&NHX:Ev=0>1:S=
Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&&NHX:Ev=0>
1:S=Murinae:ID=AN16]):0.000[&&NHX:Ev=0>1:S=Euarchontoglires:
ID=AN12],(AN20:0.000,AN21:0.000):0.000[&&NHX:Ev=0>1:S=
Laurasiatheria:ID=AN19]):0.000[&&NHX:Ev=0>1:S=Eutheria:
ID=AN11],AN22:0.004):0.003[&&NHX:Ev=0>1:S=Mammalia:ID=AN10]
,AN23:0.000):0.014[&&NHX:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
017):0.021[&&NHX:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
066,AN28:0.052):0.010[&&NHX:Ev=1>0:ID=AN26],(AN30:0.031,
AN31:0.014):0.003[&&NHX:Ev=1>0:ID=AN29]):0.021[&&NHX:Ev=0>
1:S=Teleostei:ID=AN25]):0.147[&&NHX:Ev=0>1:S=Osteichthyes:
ID=AN7],AN32:0.194):0.104[&&NHX:Ev=0>1:S=Deuterostomia:ID=
AN6],((AN35:0.020,AN36:0.038):0.416[&&NHX:Ev=0>1:S=
Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
&NHX:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&&NHX:Ev=0>
1:S=Arthropoda:ID=AN37]):0.118[&&NHX:Ev=0>1:S=Ecdysozoa:
ID=AN33],AN42:0.381):0.594[&&NHX:Ev=0>1:S=Bilateria:ID=AN5]
,AN43:2.000):0.414[&&NHX:Ev=0>1
  :S=Eumetazoa:ID=AN4],((((((((AN52:0.484,AN53:0.427):0.418[&
&NHX:Ev=0>1:S=
Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&&NHX:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&&
NHX:Ev=0>1:S=
Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
0.186):0.143[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
0.331):0.332[&&NHX:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
ID=AN58]):0.467[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
432[&&NHX:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
AN63:0.864):0.223[&&NHX:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
0.613,AN66:0.930,AN67:0.755):0.332[&&NHX:Ev=0>1:S=
Basidiomycota:ID=AN64]):0.618[&&NHX:Ev=0>1:S=Dikarya:ID=
AN46],((((((AN74:0.337,AN75:0.406):0.298[&&NHX:Ev=0>1:S=
Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&&NHX:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&&
NHX:Ev=0>1:S=
Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:
0.403):0.191[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
0.366):0.140[&&NHX:Ev=0>1:S=Sordariomyc
  etes-Leotiomycetes:ID=AN80]):0.457[&&NHX:Ev=0>1:S=
Pezizomycotina:ID=AN78]):0.331[&&NHX:Ev=0>1:S=Pezizomycotina-
Saccharomycotina:ID=AN70],AN85:0.737):0.128[&&NHX:Ev=0>
1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&&NHX:
Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&&NHX:Ev=0>1:S=
Dikarya:ID=AN68]):0.117[&&NHX:Ev=1>0:ID=AN45],(AN90:0.984,
AN91:0.893):0.158[&&NHX:Ev=1>0:ID=AN89]):0.262[&&NHX:Ev=0>
1:S=Fungi:ID=AN44]):0.394[&&NHX:Ev=0>1:S=Opisthokonts:ID=
AN3],(AN93:0.457,AN94:0.462):0.860[&&NHX:Ev=0>1:S=
Dictyostelium:ID=AN92]):0.301[&&NHX:Ev=0>1:S=Unikonts:ID=
AN2],AN95:1.440,AN96:2.000):2.000[&&NHX:Ev=0>1:S=Eukaryota:
ID=AN1])[&&NHX:Ev=1>0:ID=AN0];

I get the following error: "The tree has apparently singleton node(s):
cannot read tree file.  Reading Newick file aborted at tree no. 1",
which seems to be wrong since I can actually read this tree without
problem
using rncl::read_newick_phylo and this online tool
http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e
9f&algid=ce443ed1e53858bf4e11d1e069c7a927

I understand that this particular tree is a modified version of Newick's
format, but this is the first time that I have problems reading this
type
of tree.

Here my session info:

devtools::session_info()

Session info
------------------------------------------------------------
-----------------------------------------------------------------
  setting  value
  version  R version 3.4.1 (2017-06-30)
  system   x86_64, linux-gnu
  ui       RStudio (1.0.143)
  language (EN)
  collate  en_US.UTF-8
  tz       America/New_York
  date     2017-09-05

Packages
------------------------------------------------------------
---------------------------------------------------------------------
  package     * version date       source
  ape           4.1     2017-02-14 CRAN (R 3.4.0)
  assertthat    0.2.0   2017-04-11 CRAN (R 3.4.0)
  base        * 3.4.1   2017-06-30 local
  compiler      3.4.1   2017-06-30 local
  datasets    * 3.4.1   2017-06-30 local
  devtools      1.13.3  2017-08-02 CRAN (R 3.4.0)
  digest        0.6.12  2017-01-27 CRAN (R 3.4.0)
  graphics    * 3.4.1   2017-06-30 local
  grDevices   * 3.4.1   2017-06-30 local
  grid          3.4.1   2017-06-30 local
  lattice       0.20-35 2017-03-25 CRAN (R 3.4.1)
  magrittr      1.5     2014-11-22 CRAN (R 3.4.0)
  memoise       1.1.0   2017-04-21 CRAN (R 3.4.0)
  methods     * 3.4.1   2017-06-30 local
  nlme          3.1-131 2017-02-06 CRAN (R 3.4.1)
  parallel      3.4.1   2017-06-30 local
  prettyunits   1.0.2   2015-07-13 CRAN (R 3.4.1)
  progress      1.1.2   2016-12-14 CRAN (R 3.4.1)
  R6            2.2.2   2017-06-17 CRAN (R 3.4.0)
  Rcpp          0.12.12 2017-07-15 CRAN (R 3.4.0)
  rncl          0.8.2   2016-12-16 CRAN (R 3.4.1)
  stats       * 3.4.1   2017-06-30 local
  tools         3.4.1   2017-06-30 local
  utils       * 3.4.1   2017-06-30 local
  withr         2.0.0   2017-07-28 CRAN (R 3.4.0)


Any ideas?

Best,

George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon

         [[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-ph...@r-project.org/

         [[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-ph...@r-project.org/

         [[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-ph...@r-project.org/

_______________________________________________
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-ph...@r-project.org/




--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/


        [[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 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] Possible Bug in ape::read.tree

Reply via email to