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

[PIKAL Petr]

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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> PLEASE do read the posting guide http://www.R-project.org/posting-
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> and provide commented, minimal, self-contained, reproducible code.

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