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.ste...@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 <ama...@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.pi...@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-boun...@r-project.org] On Behalf Of Aman > >>> Gill > >>> Sent: Thursday, March 12, 2015 6:08 PM > >>> To: r-help@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]] > >>> > >>> ______________________________________________ > >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>> https://stat.ethz.ch/mailman/listinfo/r-help > >>> PLEASE do read the posting guide http://www.R-project.org/posting- > >>> guide.html > >>> and provide commented, minimal, self-contained, reproducible code. > >> > >> ________________________________ > >> Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou > >> určeny pouze jeho adresátům. > >> Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě > >> neprodleně jeho odesílatele. 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