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. Obsah tohoto emailu i s přílohami a jeho kopie > vymažte ze svého systému. > Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email > jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. > Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi > či zpožděním přenosu e-mailu. > > V případě, že je tento e-mail součástí obchodního jednání: > - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření > smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. > - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; > Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany > příjemce s dodatkem či odchylkou. > - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve > výslovným dosažením shody na všech jejích náležitostech. > - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za > společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn > nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto > emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich > existence je adresátovi či osobě jím zastoupené známá. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. > [[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.
