I am not an expert in the area, but I think 0 and 100 are not allowed in the data frame. I generated a fake dataset, with one row with 0 and 100 (and each row adds up to 100, 200*6), I got a message that "n<=p, are you serious?". LOL. When I generated a data set with non-zero proportions, everything seems working fine. I am kind of curious why you chose this method. :) Shuyu
On Sep 8, 2017 03:03, <r-sig-robust-request at r-project.org> wrote:
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https://stat.ethz.ch/mailman/listinfo/r-sig-robust or, via email, send a message with subject or body 'help' to r-sig-robust-request at r-project.org You can reach the person managing the list at r-sig-robust-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-SIG-Robust digest..." Today's Topics: 1. Re: robust PCA in robComposition (Alice Domalik) ---------------------------------------------------------------------- Message: 1 Date: Thu, 7 Sep 2017 06:21:05 -0700 (PDT) From: Alice Domalik <adomalik at sfu.ca> To: Filzmoser Peter <peter.filzmoser at tuwien.ac.at> Cc: r-sig-robust at r-project.org Subject: Re: [RsR] robust PCA in robComposition Message-ID: <2124604615.78038283.1504790465732.JavaMail.zimbra at sfu.ca> Content-Type: text/plain; charset="UTF-8" My data set includes lots of zeros and 100's. I thought that might be the problem, but I could find anything in the documentation about requirements for the data frame. Alice From: "Filzmoser Peter" <peter.filzmoser at tuwien.ac.at> To: "Alice Domalik" <adomalik at sfu.ca>, r-sig-robust at r-project.org Sent: Wednesday, September 6, 2017 8:26:40 PM Subject: Re: robust PCA in robComposition Hard to say without no more details about the data frame. Maybe there are zeros included? Best regards, Peter ------------------------------------------------------------ ------------------ Prof. Dr. Peter Filzmoser CSTAT - Computational Statistics Institute of Statistics & Mathematical Methods in Economics Vienna University of Technology Wiedner Hauptstr. 8-10 1040 Vienna, Austria (DVR: 0005886) Tel. +43 1 58801 10560 FAX +43 1 58801 105699 e-mail: P.Filzmoser at tuwien.ac.at http://www.statistik.tuwien.ac.at/public/filz/ ------------------------------------------------------------ ------------------ ________________________________________ From: R-SIG-Robust <r-sig-robust-bounces at r-project.org> on behalf of Alice Domalik <adomalik at sfu.ca> Sent: Thursday, September 7, 2017 3:13 AM To: r-sig-robust at r-project.org Subject: [RsR] robust PCA in robComposition I am trying to perform a robust PCA analysis on compositional data. My data set includes 400 diet samples from a species of predatory fish. For each sample, I have the percent of the diet that is comprised of 7 species of prey item. Each row sums to 100. sandlance rockfish salmon saury anchovy herring squid 100.00000 0.00000 0.00000 0.00000 0 0.000000 0.00000 100.00000 0.00000 0.00000 0.00000 0 0.000000 0.00000 75.00000 0.00000 0.00000 0.00000 0 25.000000 0.00000 I tried "pcaCoDa(diet.df)" (from the package robComposition), b ut I get the following error: Error in x.ilr[, i] <- sqrt((i)/(i + 1)) * log(((apply(as.matrix(x[, 1:i]), : incorrect number of subscripts on matrix What does this error mean and how can I resolve the problem? [[alternative HTML version deleted]] _______________________________________________ R-SIG-Robust at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-robust [[alternative HTML version deleted]] ------------------------------ Subject: Digest Footer _______________________________________________ R-SIG-Robust mailing list R-SIG-Robust at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-robust ------------------------------ End of R-SIG-Robust Digest, Vol 87, Issue 2 *******************************************