[R] Help with error: arguments imply differing number of rows

Sat Mar 14 16:34:12 CET 2015

Thanks for the reply. The results of str() are indeed the same. Is there
anything else I can check that might explain the difference?

> str(phyl_tree)
List of 4
 $ edge       : int [1:15, 1:2] 10 11 12 13 14 14 13 12 15 15 ...
 $ Nnode      : int 7
 $ tip.label  : chr [1:9] "Heliantheae" "Eupatorieae" "Helenieae"
"Gnaphalieae" ...
 $ edge.length: num [1:15] 1 1 1 1 1 1 2 1 2 1 ...
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"
>
> str(chem_tree)
List of 4
 $ edge       : int [1:15, 1:2] 10 11 12 13 14 15 15 14 16 16 ...
 $ Nnode      : int 7
 $ tip.label  : chr [1:9] "Heliantheae" "Helenieae" "Eupatorieae"
"Astereae" ...
 $ edge.length: num [1:15] 1 2 1 1 1 1 1 1 1 1 ...
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"

> str(phyl_data)
 int [1:35, 1:9] 0 0 0 1 0 0 0 0 0 1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:35] "Uroleucon_aeneum" "Uroleucon_aff_atripes"
"Uroleucon_amamianum" "Uroleucon_ambrosiae" ...
  ..$ : chr [1:9] "Heliantheae" "Eupatorieae" "Helenieae" "Gnaphalieae" ...
>
> str(chem_data)
 int [1:35, 1:9] 0 0 0 1 0 0 0 0 0 1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:35] "Uroleucon_aeneum" "Uroleucon_aff_atripes"
"Uroleucon_amamianum" "Uroleucon_ambrosiae" ...
  ..$ : chr [1:9] "Heliantheae" "Helenieae" "Eupatorieae" "Astereae" ...

On Fri, Mar 13, 2015 at 7:31 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:

> Hi
>
> Without further information you probably do not get answers. Everything
> seems to be same so the only reason can be that the objects seems to be
> same but they have some inner distinctions, maybe type of variables.
>
> Are results of
>
> str(your.objects)
>
> same in equivalent objects?
>
> Cheers
> Petr
>
> > -----Original Message-----
> > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Aman
> > Gill
> > Sent: Thursday, March 12, 2015 6:08 PM
> > To: r-help at r-project.org
> > Subject: [R] Help with error: arguments imply differing number of rows
> >
> > Hello,
> >
> > I am stuck trying to run an analysis using the package picante. I am
> > running two very similar analyses. One works as expected, but when I
> > try
> > the other, I get the error:
> >
> > Error in data.frame(PD = PDs, SR = SR) :
> >   arguments imply differing number of rows: 34, 35
> >
> > This is strange to me since the data matrix is the same for both
> > analyses
> > (numbers of rows and columns are the same; the only difference is the
> > order
> > of the columns). Each analyses requires a phylogenetic tree (.tre
> > file),
> > and each tree is very similar. Any thoughts as to what's causing this
> > problem? The problem may be specific to the function I'm using [pd()],
> > but
> > since the error is a data.frame error I thought I'd ask here. Here is
> > the
> > code I'm using:
> >
> > This works:
> > phyl_tree <- read.nexus("phyl.tre")
> > phyl_data <- as.matrix(read.table("phyl_matrix.txt"), header=TRUE, sep
> > =
> > "\t")
> > pd.result <- pd(phyl_data, phyl_tree, include.root = TRUE)
> >
> > This fails (this matrix.txt file is the same as above, except that
> > columns
> > are ordered to match the tree; I have also used the above matrix.txt
> > file)
> > chem_tree <- read.nexus("chem.tre")
> > chem_data <- as.matrix(read.table("chem_matrix.txt"), header=TRUE, sep
> > =
> > "\t")
> > pd_chem.result <- pd(chem_data, chem_tree, include.root = TRUE)
> >
> > ERROR:
> > Error in data.frame(PD = PDs, SR = SR) :
> >   arguments imply differing number of rows: 34, 35
> >
> >
> > To illustrate that the data for each run are very similar (row and
> > column
> > names are also the same in both data files):
> >
> > > phyl_tree
> >
> > Phylogenetic tree with 9 tips and 7 internal nodes.
> >
> > Tip labels:
> > Heliantheae, Eupatorieae, Helenieae, Gnaphalieae, Anthemideae,
> > Astereae, ...
> > Node labels:
> > root, minCyn, minCic, HelEurHel, HelEur, GnaAnthAst, ...
> >
> > Rooted; includes branch lengths.
> >
> > > nrow(phyl_data)
> > [1] 35
> > > ncol(phyl_data)
> > [1] 9
> > > class(phyl_data)
> > [1] "matrix"
> >
> >
> > > chem_tree
> >
> > Phylogenetic tree with 9 tips and 7 internal nodes.
> >
> > Tip labels:
> > Heliantheae, Helenieae, Eupatorieae, Astereae, Gnaphlieae, Senecioneae,
> > ...
> > Node labels:
> > root, minC, minAnth, minSen, minGna, HelHel, ...
> >
> > Rooted; includes branch lengths.
> >
> > > nrow(chem_data)
> > [1] 35
> > > ncol(chem_data)
> > [1] 9
> > > class(chem_data)
> > [1] "matrix"
> >
> >       [[alternative HTML version deleted]]
> >
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