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

Wed Mar 18 21:47:18 CET 2015

I did notice those differences, but I presumed they reflected different
values in each of the two objects, rather than a difference in the
structure of the objects, which I assume to be the cause of the error. For
example, the "tip.label" structure for each object is the same [1:9]
although each has different values (plant tribe names).

Would you mind explaining how these differences might pertain to the error
of "arguments imply differing number of rows"? I am not a very experienced
R user so I may be missing something here.

On Sat, Mar 14, 2015 at 11:44 AM, Boris Steipe <boris.steipe at utoronto.ca>
wrote:

> Not the same. Read carefully...
>
> > $ edge       : int [1:15, 1:2] 10 11 12 13 14 14 13 12 15 15 ...
> > $ edge       : int [1:15, 1:2] 10 11 12 13 14 15 15 14 16 16 ...
>                                                 ^^... etc
>
> B.
>
>
> On Mar 14, 2015, at 11:34 AM, Aman Gill <amango at gmail.com> wrote:
>
> > 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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