subject:"\[R\-sig\-phylo\] Bug in ape\?"

Re: [R-sig-phylo] Bug in ape?

2017-04-28 Thread François Michonneau

Hi Simon and others,

  I ran into the same problems a few days ago and I suspect it's
related to changes associated with R 3.4.0. Re-installing ape solved
the issue for me.

  Cheers,
  -- François

On Wed, Apr 26, 2017 at 11:01 PM, Simon Blomberg  wrote:
> False alarm. I cleared my workspace and re-started R and the problem has
> gone away. I'm curious to know how it occurred but I'm happy that it has
> been resolved. We now return you to your scheduled R programming...
>
> Cheers,
>
> Simon.
>
>
>
> On 27/04/17 12:44, Simon Blomberg wrote:
>>
>> Hi Emmanuel and other list members.
>>
>> I am having some problems creating and working with trees (phylo objects)
>> in ape. Has anyone else seen this error? The following code reproduces the
>> errors:
>>
>> library(ape)
>> tr1 <- rtree(10)
>>
>> plot(tr1)
>>
>> Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
>>   object 'neworder_phylo' not found
>>
>> tr2 <- rcoal(10)
>>
>> Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
>>   object 'neworder_phylo' not found
>>
>> tr3 <- read.tree(text="((a, b), (c, d));")
>>
>> compute.brlen(tr3)
>>
>> Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
>>   object 'neworder_phylo' not found
>>
>> ## All have the same traceback:
>>
>> > traceback()
>> 4: .reorder_ape(x, order, index.only, length(x$tip.label), io)
>> 3: reorder.phylo(phy, "postorder")
>> 2: reorder(phy, "postorder")
>> 1: compute.brlen(tr3)
>>
>> > sessionInfo()
>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 17.04
>>
>> Matrix products: default
>> BLAS: /usr/lib/openblas-base/libblas.so.3
>> LAPACK: /usr/lib/libopenblasp-r0.2.19.so
>>
>> locale:
>>  [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C
>>  [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
>>  [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
>>  [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C
>>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods base
>>
>> other attached packages:
>> [1] ape_4.1
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.10 magrittr_1.5 splines_3.4.0 MASS_7.3-47
>>  [5] munsell_0.4.3colorspace_1.3-2 lattice_0.20-35 minqa_1.2.4
>>  [9] stringr_1.2.0glmmADMB_0.8.3.3 plyr_1.8.4 tcltk_3.4.0
>> [13] tools_3.4.0  parallel_3.4.0   nnet_7.3-12 grid_3.4.0
>> [17] nlme_3.1-131 gtable_0.2.0 coda_0.19-1 fortunes_1.5-4
>> [21] lme4_1.1-13  lazyeval_0.2.0   tibble_1.3.0 Matrix_1.2-8
>> [25] R2admb_0.7.15nloptr_1.0.4 ggplot2_2.2.1 effects_3.1-2
>> [29] stringi_1.1.5compiler_3.4.0   scales_0.4.1
>>
>> I am not getting the error on two other machines with the same OS and (as
>> far as I can tell) the same setup. Any help would be greatly appreciated!
>>
>> Cheers,
>>
>> Simon.
>>
>
> --
> Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
> Senior Lecturer and Consultant Statistician
> School of Biological Sciences
> The University of Queensland
> St. Lucia Queensland 4072
> Australia
> T: +61 7 3365 2506
> email: S.Blomberg1_at_uq.edu.au
> http://www.evolutionarystatistics.org
>
> Policies:
> 1.  I will NOT analyse your data for you.
> 2.  Your deadline is your problem.
>
> Basically, I'm not interested in doing research and
> I never have been. I'm interested in understanding,
> which is quite a different thing. And often to
> understand something you have to work it out for
> yourself because no one else has done it.
> - David Blackwell
>
> ___
> 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] Bug in ape?

2017-04-26 Thread Simon Blomberg

False alarm. I cleared my workspace and re-started R and the problem has 
gone away. I'm curious to know how it occurred but I'm happy that it has 
been resolved. We now return you to your scheduled R programming...


Cheers,

Simon.


On 27/04/17 12:44, Simon Blomberg wrote:

Hi Emmanuel and other list members.

I am having some problems creating and working with trees (phylo 
objects) in ape. Has anyone else seen this error? The following code 
reproduces the errors:


library(ape)
tr1 <- rtree(10)

plot(tr1)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

tr2 <- rcoal(10)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

tr3 <- read.tree(text="((a, b), (c, d));")

compute.brlen(tr3)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

## All have the same traceback:

> traceback()
4: .reorder_ape(x, order, index.only, length(x$tip.label), io)
3: reorder.phylo(phy, "postorder")
2: reorder(phy, "postorder")
1: compute.brlen(tr3)

> sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

other attached packages:
[1] ape_4.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 magrittr_1.5 splines_3.4.0 MASS_7.3-47
 [5] munsell_0.4.3colorspace_1.3-2 lattice_0.20-35 minqa_1.2.4
 [9] stringr_1.2.0glmmADMB_0.8.3.3 plyr_1.8.4 tcltk_3.4.0
[13] tools_3.4.0  parallel_3.4.0   nnet_7.3-12 grid_3.4.0
[17] nlme_3.1-131 gtable_0.2.0 coda_0.19-1 fortunes_1.5-4
[21] lme4_1.1-13  lazyeval_0.2.0   tibble_1.3.0 Matrix_1.2-8
[25] R2admb_0.7.15nloptr_1.0.4 ggplot2_2.2.1 effects_3.1-2
[29] stringi_1.1.5compiler_3.4.0   scales_0.4.1

I am not getting the error on two other machines with the same OS and 
(as far as I can tell) the same setup. Any help would be greatly 
appreciated!


Cheers,

Simon.



--
Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au
http://www.evolutionarystatistics.org

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

Basically, I'm not interested in doing research and
I never have been. I'm interested in understanding,
which is quite a different thing. And often to
understand something you have to work it out for
yourself because no one else has done it.
- David Blackwell

___
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] Bug in ape?

2017-04-26 Thread Simon Blomberg


Hi Emmanuel and other list members.

I am having some problems creating and working with trees (phylo 
objects) in ape. Has anyone else seen this error? The following code 
reproduces the errors:


library(ape)
tr1 <- rtree(10)

plot(tr1)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

tr2 <- rcoal(10)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

tr3 <- read.tree(text="((a, b), (c, d));")

compute.brlen(tr3)

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
  object 'neworder_phylo' not found

## All have the same traceback:

> traceback()
4: .reorder_ape(x, order, index.only, length(x$tip.label), io)
3: reorder.phylo(phy, "postorder")
2: reorder(phy, "postorder")
1: compute.brlen(tr3)

> sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

other attached packages:
[1] ape_4.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 magrittr_1.5 splines_3.4.0 MASS_7.3-47
 [5] munsell_0.4.3colorspace_1.3-2 lattice_0.20-35 minqa_1.2.4
 [9] stringr_1.2.0glmmADMB_0.8.3.3 plyr_1.8.4 tcltk_3.4.0
[13] tools_3.4.0  parallel_3.4.0   nnet_7.3-12 grid_3.4.0
[17] nlme_3.1-131 gtable_0.2.0 coda_0.19-1 fortunes_1.5-4
[21] lme4_1.1-13  lazyeval_0.2.0   tibble_1.3.0 Matrix_1.2-8
[25] R2admb_0.7.15nloptr_1.0.4 ggplot2_2.2.1 effects_3.1-2
[29] stringi_1.1.5compiler_3.4.0   scales_0.4.1

I am not getting the error on two other machines with the same OS and 
(as far as I can tell) the same setup. Any help would be greatly 
appreciated!


Cheers,

Simon.

--

Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au
http://www.evolutionarystatistics.org

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

Basically, I'm not interested in doing research and
I never have been. I'm interested in understanding,
which is quite a different thing. And often to
understand something you have to work it out for
yourself because no one else has done it.
- David Blackwell

___
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] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

2015-08-17 Thread David Bapst

Hi Emannuel (and list),

Just wanted to let you know that after some testing with my own cases,
the new drop.tip appears to fix the error, so the issue is closed from
my perspective.

Cheers,
-Dave

On Tue, Jul 28, 2015 at 12:25 PM, Emmanuel Paradis
emmanuel.para...@ird.fr wrote:
 Hi David,

 I've conducted more tests and the bug was really in drop.tip and sometimes
 apparent without calling ladderize. The fix seems to work well. I have built
 ape 3.3-0.6 which is available on ape-package.ird.fr as source package.

 Best,

 Emmanuel


 Le 25/07/2015 19:33, Emmanuel Paradis a écrit :

 David,

 I was thinking about some simple tests to check that the function still
 works correctly in other situations. It can happen that when fixing a
 bug which occurs in a special situation in a piece of code, the code
 then fails in other (possibly simpler) situations. In the present case,
 the fix is the part of the code that renumbers the nodes which is thus
 used in all cases (even if there are no node labels). I'll conduct some
 tests later, but in the mean time if you see something strange, just
 tell me.

 I attach the new source file.

 Best,

 Emmanuel

 Le 25/07/2015 18:54, David Bapst a écrit :

 Hi Emmanuel,

 Thank you for the fix! And, yes, I realize, its probably one of ape's
 most widely used functions. Perhaps what we need is a function that
 tests whether there is a mismatch in the node.labels, across trees
 that might have different sets of taxa, which will help in the future
 to alert us if this bug appears again. Of course, such a function
 would need to avoid using drop.tip entirely. I've looked and I'm not
 aware of any function across the entire Phylogenetics taskview that
 fulfills this criteria.

 So, I admit that's a tough order. I've made a particularly ugly first
 stab at such a thing, mostly depending on prop.part. Its rather
 clumsy, as I originally wrote it as code to fix node.labels, rather
 than find the mismatches. Unfortunately, at present, it misidentifies
 root-ward losses of clades, due to dropping of stem/out-group tips, as
 a mismatch between node labels. Perhaps someone else will see a
 cleaner, more accurate solution.


 ###


 library(ape)

 testNodeLabels-function(tree1,tree2,printMisMatch=TRUE,plot=FALSE){
  nlab1-tree1$node.label
  if(!is.null(tree2$node.label)){
  nlab2-tree2$node.label
  }else{
  nlab2-rep(NA,Nnode(tree2))
  }
  #if tree2 has any taxa not in tree1, stop
  noMatch-sapply(tree2$tip.label,function(x)
 !any(x==tree1$tip.label))
  if(any(noMatch)){
  stop(tree2 has taxa not found in tree1 and thus is
 uncomparable)
  }
  #
  desc1-lapply(prop.part(tree1),function(x) tree1$tip.label[x])
  desc2-lapply(prop.part(tree2),function(x) tree2$tip.label[x])
  #need to remove taxa not shared by one without using drop.tip
  taxa-c(tree1$tip.label,tree2$tip.label)
  shared-taxa[sapply(taxa,function(x)
  any(x==tree1$tip.label)  any(x==tree2$tip.label))]
  #get ndesc for desc2
  ndesc2-sapply(desc2,length)
  #reorder desc2 and nlab2
  desc2-desc2[order(ndesc2)]
  nlab2-nlab2[order(ndesc2)]
  result-TRUE
  for(i in 1:length(desc1)){
  target-desc1[[i]]
  targetName-nlab1[i]
  sharedDesc-target[sapply(target,function(x)
  any(x==shared))]
  if(length(sharedDesc)1){
  #find matches in 2
  matches-sapply(desc2,function(x)
  all(sapply(sharedDesc,function(z) any(z==x
  }else{
  matches-FALSE
  }
  #get richest match - if there is no match, get NA
  matchClade-which(matches)[1]
  if(!is.na(matchClade)){
  matchName-identical(nlab1[i],nlab2[matchClade])
  if(!matchName){
  result-FALSE
  if(printMisMatch){
  warning(paste(\n A node with descendants:,
  paste0(sharedDesc,collapse=', '),
  \n is labeled:,nlab1[i],
  in tree1 but labeled:,
  nlab2[matchClade],in tree2 \n))
  }
  }
  }
  }
  #
  if(plot){
  #plot it
  layout(1:2)
  plot(tree1,show.tip.label=TRUE,use.edge.length=FALSE)
  nodelabels(tree1$node.label)
  plot(tree2,show.tip.label=TRUE,use.edge.length=FALSE)
  nodelabels(tree2$node.label)
  layout(1)
  }
  return(result)
  }

 set.seed(1)
 tree-rtree(10)
 tree$node.label-rep(NA,Nnode(tree))
 tree$node.label[1]-ROOT
 tree$node.label[5]-HELLO
 tree$node.label[8]-NOPE

 tree1-drop.tip(tree,t2)
 tree2-ladderize(tree)
 tree3-drop.tip(tree2,t2)

 testNodeLabels(tree,tree1)
 testNodeLabels(tree,tree2)
 testNodeLabels(tree,tree3)

Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

2015-07-28 Thread Emmanuel Paradis


Hi David,

I've conducted more tests and the bug was really in drop.tip and 
sometimes apparent without calling ladderize. The fix seems to work 
well. I have built ape 3.3-0.6 which is available on ape-package.ird.fr 
as source package.


Best,

Emmanuel

Le 25/07/2015 19:33, Emmanuel Paradis a écrit :

David,

I was thinking about some simple tests to check that the function still
works correctly in other situations. It can happen that when fixing a
bug which occurs in a special situation in a piece of code, the code
then fails in other (possibly simpler) situations. In the present case,
the fix is the part of the code that renumbers the nodes which is thus
used in all cases (even if there are no node labels). I'll conduct some
tests later, but in the mean time if you see something strange, just
tell me.

I attach the new source file.

Best,

Emmanuel

Le 25/07/2015 18:54, David Bapst a écrit :

Hi Emmanuel,

Thank you for the fix! And, yes, I realize, its probably one of ape's
most widely used functions. Perhaps what we need is a function that
tests whether there is a mismatch in the node.labels, across trees
that might have different sets of taxa, which will help in the future
to alert us if this bug appears again. Of course, such a function
would need to avoid using drop.tip entirely. I've looked and I'm not
aware of any function across the entire Phylogenetics taskview that
fulfills this criteria.

So, I admit that's a tough order. I've made a particularly ugly first
stab at such a thing, mostly depending on prop.part. Its rather
clumsy, as I originally wrote it as code to fix node.labels, rather
than find the mismatches. Unfortunately, at present, it misidentifies
root-ward losses of clades, due to dropping of stem/out-group tips, as
a mismatch between node labels. Perhaps someone else will see a
cleaner, more accurate solution.

###


library(ape)

testNodeLabels-function(tree1,tree2,printMisMatch=TRUE,plot=FALSE){
 nlab1-tree1$node.label
 if(!is.null(tree2$node.label)){
 nlab2-tree2$node.label
 }else{
 nlab2-rep(NA,Nnode(tree2))
 }
 #if tree2 has any taxa not in tree1, stop
 noMatch-sapply(tree2$tip.label,function(x)
!any(x==tree1$tip.label))
 if(any(noMatch)){
 stop(tree2 has taxa not found in tree1 and thus is
uncomparable)
 }
 #
 desc1-lapply(prop.part(tree1),function(x) tree1$tip.label[x])
 desc2-lapply(prop.part(tree2),function(x) tree2$tip.label[x])
 #need to remove taxa not shared by one without using drop.tip
 taxa-c(tree1$tip.label,tree2$tip.label)
 shared-taxa[sapply(taxa,function(x)
 any(x==tree1$tip.label)  any(x==tree2$tip.label))]
 #get ndesc for desc2
 ndesc2-sapply(desc2,length)
 #reorder desc2 and nlab2
 desc2-desc2[order(ndesc2)]
 nlab2-nlab2[order(ndesc2)]
 result-TRUE
 for(i in 1:length(desc1)){
 target-desc1[[i]]
 targetName-nlab1[i]
 sharedDesc-target[sapply(target,function(x)
 any(x==shared))]
 if(length(sharedDesc)1){
 #find matches in 2
 matches-sapply(desc2,function(x)
 all(sapply(sharedDesc,function(z) any(z==x
 }else{
 matches-FALSE
 }
 #get richest match - if there is no match, get NA
 matchClade-which(matches)[1]
 if(!is.na(matchClade)){
 matchName-identical(nlab1[i],nlab2[matchClade])
 if(!matchName){
 result-FALSE
 if(printMisMatch){
 warning(paste(\n A node with descendants:,
 paste0(sharedDesc,collapse=', '),
 \n is labeled:,nlab1[i],
 in tree1 but labeled:,
 nlab2[matchClade],in tree2 \n))
 }
 }
 }
 }
 #
 if(plot){
 #plot it
 layout(1:2)
 plot(tree1,show.tip.label=TRUE,use.edge.length=FALSE)
 nodelabels(tree1$node.label)
 plot(tree2,show.tip.label=TRUE,use.edge.length=FALSE)
 nodelabels(tree2$node.label)
 layout(1)
 }
 return(result)
 }

set.seed(1)
tree-rtree(10)
tree$node.label-rep(NA,Nnode(tree))
tree$node.label[1]-ROOT
tree$node.label[5]-HELLO
tree$node.label[8]-NOPE

tree1-drop.tip(tree,t2)
tree2-ladderize(tree)
tree3-drop.tip(tree2,t2)

testNodeLabels(tree,tree1)
testNodeLabels(tree,tree2)
testNodeLabels(tree,tree3)

testNodeLabels(tree,tree3,plot=TRUE)



Additionally, could you send the full revised source file? I have to
admit, I always get lost looking for ape's newest source files on the
ape website.

Cheers,
-Dave

On Sat, Jul 25, 2015 at 6:20 AM, Emmanuel Paradis
emmanuel.para...@ird.fr wrote:

Hi David,

Here is a fix for drop.tip (line numbers refer to the source

[R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

2015-07-17 Thread David Bapst

Hello all,

Recently I noticed a complex function of mine that does some tree
transformations was randomly scrambling node.label elements.

In the course of doing so, I found this old email (below) from Rebecca
Best in 2012, which outlined an issue that occurred when a ladderized
tree had tips dropped. It appears that bug has reappeared  in more
recent version of ape.

Here's a slightly modified version of her example code, which appears
to still replicate a node label shuffling in ape v3.3.

#
require(ape)

#read tree
mytree-read.tree()
((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1);

#ladderize tree
mytree.lad-ladderize(mytree)

#node labels display on both trees correctly
layout(1:2)
plot(mytree,show.node.label=TRUE)
plot(mytree.lad,show.node.label=TRUE)

#drop tips from both trees
drop.mytree-drop.tip(mytree,c(L,D,G))
drop.mytree.lad-drop.tip(mytree.lad,c(L,D,G))

#plot both trees, node labels are incorrect for ladderized tree
dev.new()
layout(1:2)
plot(drop.mytree,show.node.label=TRUE)
plot(drop.mytree.lad,show.node.label=TRUE)
#

Although I'm still in the process of dismantling my own issue, so I am
not 100% certain, I strongly believe this is the culprit in my case,
as my script partly drops.tips from an input tree (that happens to
always be ladderized).

Cheers,
-Dave


-- Forwarded message --
From: Rebecca Best rjb...@ucdavis.edu
Date: Tue, Oct 2, 2012 at 12:26 AM
Subject: [R-sig-phylo] ladderize + drop.tip = shuffled node labels
To: r-sig-phylo@r-project.org


Hi all

I have been plotting some pruned trees recently, and have run into a
problem using drop.tip() after ladderize(). If you ladderize() and
then drop tips from the ladderized tree, then at least in my case the
node labels are no longer correct. This may be an unlikely sequence of
commands, but I thought I'd post this in case it is an easy fix, or it
helps anyone else avoid issues.
Thanks!

Rebecca

##

require(ape)

#read tree

mytree-read.tree()
((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1);

#ladderize tree

mytree.lad-ladderize(mytree)

#node labels display on both trees correctly

plot(mytree,show.node.label=TRUE)
plot(mytree.lad,show.node.label=TRUE)

#drop tips from both trees

drop.mytree-drop.tip(mytree,c(L,D,G))
drop.mytree.lad-drop.tip(mytree.lad,c(L,D,G))

#plot both trees, node labels are incorrect for ladderized tree

plot(drop.mytree,show.node.label=TRUE)
plot(drop.mytree.lad,show.node.label=TRUE)

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-- 
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701

http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html

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Re: [R-sig-phylo] Bug in ape?

Re: [R-sig-phylo] Bug in ape?

[R-sig-phylo] Bug in ape?

Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

[R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

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