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

2017-09-08 Thread Emmanuel Paradis

Hi George,

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


R> write.tree(rtree(5), 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 
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 
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"  wrote:

Hi,

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

((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
,AN43:2.000):0.414[&:Ev=0>1
  :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&
:Ev=0>1:S=
Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&: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[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&: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[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
0.366):0.140[&:Ev=0>1:S=Sordariomyc
  etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>

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

2017-09-07 Thread George Vega Yon
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 
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 
> 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"  wrote:

 Hi,

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

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

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

2017-09-05 Thread Klaus Schliep
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  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"  wrote:
>>>
>>> Hi,
>>>
>>> When trying to read this tree with the ape::read.tree function :
>>>
>>> ((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
>>> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
>>> 1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
>>> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
>>> Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
>>> ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
>>> ,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
>>> 017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
>>> 066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
>>> AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
>>> 1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
>>> ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
>>> AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
>>> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
>>> :Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
>>> 1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
>>> ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
>>> ,AN43:2.000):0.414[&:Ev=0>1
>>>  :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&
>>> :Ev=0>1:S=
>>> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&: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[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
>>> 0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
>>> ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
>>> 432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
>>> AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
>>> 0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
>>> Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
>>> AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
>>> Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&: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[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
>>> 0.366):0.140[&:Ev=0>1:S=Sordariomyc
>>>  etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
>>> Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
>>> Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>
>>> 1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:
>>> Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=
>>> Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,
>>> AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>
>>> 1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=
>>> AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=
>>> Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=
>>> AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:
>>> ID=AN1])[&: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=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
>>> 

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

2017-09-05 Thread Liam J. Revell
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"  wrote:

Hi,

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

((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
,AN43:2.000):0.414[&:Ev=0>1
 :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&:Ev=0>1:S=
Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&:Ev=0>1:S=
Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&:Ev=0>1:S=
Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:
0.403):0.191[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
0.366):0.140[&:Ev=0>1:S=Sordariomyc
 etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>
1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:
Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=
Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,
AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>
1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=
AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=
Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=
AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:
ID=AN1])[&: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=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)
 assertthat0.2.0   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)
 digest0.6.12  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 

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

2017-09-05 Thread George Vega Yon
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"  wrote:
>
> Hi,
>
> When trying to read this tree with the ape::read.tree function :
>
> ((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
> 1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
> Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
> ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
> ,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
> 017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
> 066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
> AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
> 1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
> ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
> AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
> :Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
> 1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
> ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
> ,AN43:2.000):0.414[&:Ev=0>1
>  :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&:Ev=0>1:S=
> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>
> 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&:Ev=0>1:S=
> Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
> 0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
> 0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
> ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
> 432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
> AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
> 0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
> Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
> AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
> Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&:Ev=0>
> 1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&:Ev=0>1:S=
> Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:
> 0.403):0.191[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
> 0.366):0.140[&:Ev=0>1:S=Sordariomyc
>  etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
> Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
> Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>
> 1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:
> Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=
> Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,
> AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>
> 1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=
> AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=
> Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=
> AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:
> ID=AN1])[&: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=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)
>  assertthat0.2.0   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)
>  digest0.6.12  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 

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

2017-09-05 Thread Mario José Marques-Azevedo
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"  wrote:

Hi,

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

((AN14:0.000,AN15:0.000):0.000[&:Ev=0>1:S=
Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&:Ev=0>
1:S=Murinae:ID=AN16]):0.000[&:Ev=0>1:S=Euarchontoglires:
ID=AN12],(AN20:0.000,AN21:0.000):0.000[&:Ev=0>1:S=
Laurasiatheria:ID=AN19]):0.000[&:Ev=0>1:S=Eutheria:
ID=AN11],AN22:0.004):0.003[&:Ev=0>1:S=Mammalia:ID=AN10]
,AN23:0.000):0.014[&:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
017):0.021[&:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
066,AN28:0.052):0.010[&:Ev=1>0:ID=AN26],(AN30:0.031,
AN31:0.014):0.003[&:Ev=1>0:ID=AN29]):0.021[&:Ev=0>
1:S=Teleostei:ID=AN25]):0.147[&:Ev=0>1:S=Osteichthyes:
ID=AN7],AN32:0.194):0.104[&:Ev=0>1:S=Deuterostomia:ID=
AN6],((AN35:0.020,AN36:0.038):0.416[&:Ev=0>1:S=
Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&:Ev=0>
1:S=Arthropoda:ID=AN37]):0.118[&:Ev=0>1:S=Ecdysozoa:
ID=AN33],AN42:0.381):0.594[&:Ev=0>1:S=Bilateria:ID=AN5]
,AN43:2.000):0.414[&:Ev=0>1
 :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&:Ev=0>1:S=
Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&:Ev=0>1:S=
Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
0.186):0.143[&:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
0.331):0.332[&:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
ID=AN58]):0.467[&:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
432[&:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],
AN63:0.864):0.223[&:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:
0.613,AN66:0.930,AN67:0.755):0.332[&:Ev=0>1:S=
Basidiomycota:ID=AN64]):0.618[&:Ev=0>1:S=Dikarya:ID=
AN46],((AN74:0.337,AN75:0.406):0.298[&:Ev=0>1:S=
Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&:Ev=0>
1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&:Ev=0>1:S=
Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:
0.403):0.191[&:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:
0.366):0.140[&:Ev=0>1:S=Sordariomyc
 etes-Leotiomycetes:ID=AN80]):0.457[&:Ev=0>1:S=
Pezizomycotina:ID=AN78]):0.331[&:Ev=0>1:S=Pezizomycotina-
Saccharomycotina:ID=AN70],AN85:0.737):0.128[&:Ev=0>
1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&:
Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&:Ev=0>1:S=
Dikarya:ID=AN68]):0.117[&:Ev=1>0:ID=AN45],(AN90:0.984,
AN91:0.893):0.158[&:Ev=1>0:ID=AN89]):0.262[&:Ev=0>
1:S=Fungi:ID=AN44]):0.394[&:Ev=0>1:S=Opisthokonts:ID=
AN3],(AN93:0.457,AN94:0.462):0.860[&:Ev=0>1:S=
Dictyostelium:ID=AN92]):0.301[&:Ev=0>1:S=Unikonts:ID=
AN2],AN95:1.440,AN96:2.000):2.000[&:Ev=0>1:S=Eukaryota:
ID=AN1])[&: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=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)
 assertthat0.2.0   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)
 digest0.6.12  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)
 R62.2.2   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