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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