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

Sat Mar 14 16:44:10 CET 2015

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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> 
> 	[[alternative HTML version deleted]]
> 
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