Re: [R-sig-phylo] Enigmatic error with drop.tip

[Juan Antonio Balbuena]

  
  
Hi Klaus and Emmanuel,
I am very grateful for your help. 

All the best
Juan Antonio


El 23/01/2017 a las 14:48, Emmanuel
  Paradis escribió:

Hi Klaus,
  
  
  Thanks for tracking this. It's fixed.
  
  
  Best,
  
  
  Emmanuel
  
  
  Le 20/01/2017 à 18:41, Klaus Schliep a écrit :
  
  Hi Juan,

it seems that you trim too many taxa.


I can replicate the error message if I trim for example 19 out
of a 20 tips

of a tree.

drop.tip(tree, sample(20, 19))

Error in integer(max(oldnodes)) : vector size cannot be infinite

In addition: Warning message:

In max(oldnodes) : no non-missing arguments to max; returning
-Inf

traceback()
  

3: integer(max(oldnodes))

2: collapse.singles(phy)

1: drop.tip(tree, sample(20, 19))


Maybe you include a check into your function z that the pruned
trees have

at least two tips left

if( length( setdiff(treeP$tip.label, colnames(hp))) < (
length(

treeP$tip.label ) -2 ) )


Cheers,

Klaus




On Fri, Jan 20, 2017 at 7:26 AM, Juan Antonio Balbuena


wrote:


Hello all
  
  
  I am working with a cophylogenetic problem where I have a host
  tree, a
  
  parasite tree and a binary matrix HP encapsulating the
  host-parasite
  
  associations . After trimming the matrix according to a given
  criterion, I
  
  require to prune the trees accordingly. Since I am getting
  errors at the
  
  execution I devised the following control function to check
  the number of
  
  tree nodes after pruning:
  
  z <- function (hp, treeH,treeP) {
  
    treeh <- drop.tip(treeH, setdiff(treeH$tip.label,
  rownames(hp)))
  
    treep <- drop.tip(treeP, setdiff(treeP$tip.label,
  colnames(hp)))
  
    res <- c(treeh$Nnode,treep$Nnode)
  
   return(res)
  
   }
  
  
  Then I try the following
  
  
  x <- sapply (THP, z, treeH=TreeH[[7]], treeP= TreeP[[7]])
  
  
  where THP is a list of trimmed HP matrices and TreeH and TreeP
  are
  
  multiphylo objects and get the following error:
  
  
  Error in integer(max(oldnodes)) : vector size cannot be
  infinite
  
  
  The traceback is
  
  
  6. integer(max(oldnodes))
  
  5. collapse.singles(phy)
  
  4. drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
  
  3. FUN(X[[i]], ...)
  
  2. lapply(X = X, FUN = FUN, ...)
  
  1. sapply(THP, z, treeH = TreeH[[7]], treeP = TreeP[[7]])
  
  
  This error appears only with this particular pair of host and
  parasite
  
  trees (#7) and I cannot find a reason why this case should be
  different.
  
  
  Any help will be very much appreciated.
  
  
  Juan A. Balbuena
  
  
  --
  
  
  Dr. Juan A. Balbuena
  
  Cavanilles Institute of Biodiversity and Evolutionary Biology
  
  University of Valencia
  
  http://www.uv.es/~balbuena
  
  P.O. Box 22085
  
  http://www.uv.es/cophylpaco
  
  
  
  46071 Valencia, Spain
  
  e-mail: j.a.balbu...@uv.es    tel. +34 963 543 658
  
  <+34%20963%2054%2036%2058>    fax +34 963 543 733
  
  <+34%20963%2054%2037%2033>
  
  
  
  *NOTE!* For shipments by EXPRESS COURIER use the following
  street address:
  
  C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
  Spain.
  
  
  
  
  ___
  
  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-
  
  

Re: [R-sig-phylo] Enigmatic error with drop.tip

[Emmanuel Paradis]

Hi Klaus,

Thanks for tracking this. It's fixed.

Best,

Emmanuel

Le 20/01/2017 à 18:41, Klaus Schliep a écrit :

Hi Juan,
it seems that you trim too many taxa.

I can replicate the error message if I trim for example 19 out of a 20 tips
of a tree.
drop.tip(tree, sample(20, 19))
Error in integer(max(oldnodes)) : vector size cannot be infinite
In addition: Warning message:
In max(oldnodes) : no non-missing arguments to max; returning -Inf

traceback()

3: integer(max(oldnodes))
2: collapse.singles(phy)
1: drop.tip(tree, sample(20, 19))

Maybe you include a check into your function z that the pruned trees have
at least two tips left
if( length( setdiff(treeP$tip.label, colnames(hp))) < ( length(
treeP$tip.label ) -2 ) )

Cheers,
Klaus



On Fri, Jan 20, 2017 at 7:26 AM, Juan Antonio Balbuena 
wrote:


Hello all

I am working with a cophylogenetic problem where I have a host tree, a
parasite tree and a binary matrix HP encapsulating the host-parasite
associations . After trimming the matrix according to a given criterion, I
require to prune the trees accordingly. Since I am getting errors at the
execution I devised the following control function to check the number of
tree nodes after pruning:
z <- function (hp, treeH,treeP) {
  treeh <- drop.tip(treeH, setdiff(treeH$tip.label, rownames(hp)))
  treep <- drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
  res <- c(treeh$Nnode,treep$Nnode)
 return(res)
 }

Then I try the following

x <- sapply (THP, z, treeH=TreeH[[7]], treeP= TreeP[[7]])

where THP is a list of trimmed HP matrices and TreeH and TreeP are
multiphylo objects and get the following error:

Error in integer(max(oldnodes)) : vector size cannot be infinite

The traceback is

6. integer(max(oldnodes))
5. collapse.singles(phy)
4. drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
3. FUN(X[[i]], ...)
2. lapply(X = X, FUN = FUN, ...)
1. sapply(THP, z, treeH = TreeH[[7]], treeP = TreeP[[7]])

This error appears only with this particular pair of host and parasite
trees (#7) and I cannot find a reason why this case should be different.

Any help will be very much appreciated.

Juan A. Balbuena

--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena
P.O. Box 22085
http://www.uv.es/cophylpaco

46071 Valencia, Spain
e-mail: j.a.balbu...@uv.estel. +34 963 543 658
<+34%20963%2054%2036%2058>fax +34 963 543 733
<+34%20963%2054%2037%2033>

*NOTE!* For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.


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Re: [R-sig-phylo] Enigmatic error with drop.tip

[Klaus Schliep]

Hi Juan,
it seems that you trim too many taxa.

I can replicate the error message if I trim for example 19 out of a 20 tips
of a tree.
drop.tip(tree, sample(20, 19))
Error in integer(max(oldnodes)) : vector size cannot be infinite
In addition: Warning message:
In max(oldnodes) : no non-missing arguments to max; returning -Inf
> traceback()
3: integer(max(oldnodes))
2: collapse.singles(phy)
1: drop.tip(tree, sample(20, 19))

Maybe you include a check into your function z that the pruned trees have
at least two tips left
if( length( setdiff(treeP$tip.label, colnames(hp))) < ( length(
treeP$tip.label ) -2 ) )

Cheers,
Klaus



On Fri, Jan 20, 2017 at 7:26 AM, Juan Antonio Balbuena 
wrote:

> Hello all
>
> I am working with a cophylogenetic problem where I have a host tree, a
> parasite tree and a binary matrix HP encapsulating the host-parasite
> associations . After trimming the matrix according to a given criterion, I
> require to prune the trees accordingly. Since I am getting errors at the
> execution I devised the following control function to check the number of
> tree nodes after pruning:
> z <- function (hp, treeH,treeP) {
>   treeh <- drop.tip(treeH, setdiff(treeH$tip.label, rownames(hp)))
>   treep <- drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
>   res <- c(treeh$Nnode,treep$Nnode)
>  return(res)
>  }
>
> Then I try the following
>
> x <- sapply (THP, z, treeH=TreeH[[7]], treeP= TreeP[[7]])
>
> where THP is a list of trimmed HP matrices and TreeH and TreeP are
> multiphylo objects and get the following error:
>
> Error in integer(max(oldnodes)) : vector size cannot be infinite
>
> The traceback is
>
> 6. integer(max(oldnodes))
> 5. collapse.singles(phy)
> 4. drop.tip(treeP, setdiff(treeP$tip.label, colnames(hp)))
> 3. FUN(X[[i]], ...)
> 2. lapply(X = X, FUN = FUN, ...)
> 1. sapply(THP, z, treeH = TreeH[[7]], treeP = TreeP[[7]])
>
> This error appears only with this particular pair of host and parasite
> trees (#7) and I cannot find a reason why this case should be different.
>
> Any help will be very much appreciated.
>
> Juan A. Balbuena
>
> --
>
> Dr. Juan A. Balbuena
> Cavanilles Institute of Biodiversity and Evolutionary Biology
> University of Valencia
> http://www.uv.es/~balbuena
> P.O. Box 22085
> http://www.uv.es/cophylpaco
> 
> 46071 Valencia, Spain
> e-mail: j.a.balbu...@uv.estel. +34 963 543 658
> <+34%20963%2054%2036%2058>fax +34 963 543 733
> <+34%20963%2054%2037%2033>
> 
> *NOTE!* For shipments by EXPRESS COURIER use the following street address:
> C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.
> 
>
> ___
> 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/

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