Re: [R] Indicator Species analysis; trouble with multipatt

2016-04-19 Thread 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.p...@gmail.com
Sent: Tue, 19 Apr 2016 08:16:54 -0400
To: jrkrid...@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 <jrkrid...@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.p...@gmail.com
 > Sent: Mon, 18 Apr 2016 16:33:54 -0400
 > To: r-help@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@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.

 
 FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
 Check it out at http://www.inbox.com/earth [http://www.inbox.com/earth]

-- 

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_
__

_Athens, GA 30602_


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__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Indicator Species analysis; trouble with multipatt

2016-04-19 Thread Ansley Silva 
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 <jrkrid...@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
> and/or 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.p...@gmail.com
> > Sent: Mon, 18 Apr 2016 16:33:54 -0400
> > To: r-help@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@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.
>
> 
> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
>
>
>


-- 
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*

*Athens, GA 30602*
install.packages("indicspecies")
library(indicspecies)

mydata<-
structure(list(necsur = structure(c(6L, 1L, 1L, 4L, 4L, 2L), .Label = c("0", 
"1", "11", "2", "24", "3", "4", "42", "5", "8", "9", "PA"), class = "factor"), 
necame = structure(c(11L, 2L, 5L, 5L, 17L, 9L), .Label = c("0", 
"1", "10", "11", "12", "13", "15", "2", "20", "22", "3", 
"4", "5", "6", "7", "8", "9", "PA"), class = "factor"), niccar = 
structure(c(1L, 
1L, 1L, 2L, 1L, 1L), .Label = c("0", "1", "19", "2", "3", 
"4", "5", "6", "PA"), class = "factor"), nicorb = structure(c(1L, 
18L, 19L, 17L, 1L, 27L), .Label = c("0", "1", "10", "11", 
"12", "13", "15", "16", "18", "19", "2", "20", "21", "23", 
"25", "29", "3", "30", "31", "32", "33", "36", "4", "40", 
"42", "44", "48", "5", "50", "6", "61", "7", "8", "9", "PA"
), class = "factor"), ni

Re: [R] Indicator Species analysis; trouble with multipatt

2016-04-19 Thread John Kane 
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
 and/or 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.p...@gmail.com
> Sent: Mon, 18 Apr 2016 16:33:54 -0400
> To: r-help@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@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.


FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!

__
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.

Re: [R] Indicator Species analysis; trouble with multipatt

2016-04-18 Thread Jim Lemon 
Hi Ansley,
Without your data file (or a meaningful subset) we can only guess, but
you may be trying to define groups on the columns rather than the rows
of the data set. Usually rows represent cases and each case must have
a value for the grouping variable.

Jim


On Tue, Apr 19, 2016 at 6:33 AM, Ansley Silva  wrote:
> 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@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.

__
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.

[R] Indicator Species analysis; trouble with multipatt

2016-04-18 Thread Ansley Silva 
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@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.