[RsR] R-SIG-Robust Digest, Vol 87, Issue 2

[Shu Yu Fan]

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 using r-project.org> wrote:

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>    1. Re:  robust PCA in robComposition (Alice Domalik)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Thu, 7 Sep 2017 06:21:05 -0700 (PDT)
> From: Alice Domalik <adomalik using sfu.ca>
> To: Filzmoser Peter <peter.filzmoser using tuwien.ac.at>
> Cc: r-sig-robust using r-project.org
> Subject: Re: [RsR] robust PCA in robComposition
> Message-ID: <2124604615.78038283.1504790465732.JavaMail.zimbra using 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 using tuwien.ac.at>
> To: "Alice Domalik" <adomalik using sfu.ca>, r-sig-robust using 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 using tuwien.ac.at
> http://www.statistik.tuwien.ac.at/public/filz/
> ------------------------------------------------------------
> ------------------
>
> ________________________________________
> From: R-SIG-Robust <r-sig-robust-bounces using r-project.org> on behalf of
> Alice Domalik <adomalik using sfu.ca>
> Sent: Thursday, September 7, 2017 3:13 AM
> To: r-sig-robust using 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?
>
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