[R] Indicator Species analysis; trouble with multipatt

[John Kane]

Hi Ansley
It looks good to me but I did not run the analysis as I am too lazy to install "indicspecies".  The inclusion of the raw data is a great help.

John Kane
Kingston ON Canada

-----Original Message-----
From: daily.puja at gmail.com
Sent: Tue, 19 Apr 2016 08:16:54 -0400
To: jrkrideau at inbox.com
Subject: Re: [R] Indicator Species analysis; trouble with multipatt

Thanks for the replies.

I have fixed the problem.  I only need to reorganized my data.  Now my question is about asking questions correctly.  I hope I've got it.  Please find the script attached here.

R Version 3.2.2

I am looking for indicator species with Indicspecies package.  After running the function multipatt, I get the following error:

Error in is.factor(x) : object 'groups1' not found

**Is this reproducibility satisfactory?  I fixed the problem by reorganizing my csv file.  I was trying to be efficient when making my groups and that was causing the trouble.

Thanks.

On Tue, Apr 19, 2016 at 6:47 AM, John Kane <jrkrideau at inbox.com> wrote:

	Hi Ansely,
 As Jim points out we really need some sample data to go with the code.

 Have a look at ?dput which is the best way to supply sample data here or have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example [http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example] and/or http://adv-r.had.co.nz/Reproducibility.html [http://adv-r.had.co.nz/Reproducibility.html] for some general suggestions on asking questions here---including discussions of using dput()

 John Kane
 Kingston ON Canada

 > -----Original Message-----
 > From: daily.puja at gmail.com
 > Sent: Mon, 18 Apr 2016 16:33:54 -0400
 > To: r-help at r-project.org
 > Subject: [R] Indicator Species analysis; trouble with multipatt
 >
 > Hello,
 >
 > *Error in tx  %*% comb : non-conformable arguments*
 >
 > Suggestions greatly appreciated.  I am a beginner and this is my first
 > time
 > posting.
 >
 > I would like to get the summary for indicator species analysis, using
 > package indicspecies with multipatt.  I am getting errors, I believe, do
 > to
 > my data organization.  After reorganizing and reorganizing, nothing has
 > helped.
 >
 >> data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",")
 >> ap<-data[c(1:24, 1:81)]
 >> groups<-c(rep(1:4,6))
 >> indval<- multipatt(ap, groups, control = how(nperm=999))
 > *Error in tx  %*% comb : non-conformable arguments*
 >
 >
 >
 > --
 > Ansley Silva
 >
 >
 > *"The clearest way into the Universe is through a forest wilderness."
 > John
 > Muir*
 >
 >
 > *Graduate Research Assistant*
 > ______________________________________________
 > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
 > https://stat.ethz.ch/mailman/listinfo/r-help [https://stat.ethz.ch/mailman/listinfo/r-help]
 > PLEASE do read the posting guide
 > http://www.R-project.org/posting-guide.html [http://www.R-project.org/posting-guide.html]
 > and provide commented, minimal, self-contained, reproducible code.

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Ansley Silva

	_
_

	_"The clearest way into the Universe is through a forest wilderness." John Muir_

	_
_

	_Graduate Research Assistant_
__

	_University of Georgia_
__

	_D.B. Warnell School of Forestry and Natural Resources_
__

	_180 East Green Street_
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	_Athens, GA 30602_

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