Dear Dr. Hamlim and other R Users,

I apologize for not stating this in my prior email, but I am working in R,
and I am using the "gowdis" function in the "FD" package and the "simprof"
function in the "clustsig" package to do my analysis. I also tried
calculating the Gower's distance matrix among my observations using "daisy"
in the package "cluster" but I philosophically like the way that "gowdis"
treats ordered/ordinal variables (i.e.,following Podani 1999's
suggestions). Regardless of using "daisy" or "gowdis", I had the same
problem.

Thank you much for requesting these clarifications.


On Sat, Jul 6, 2013 at 9:13 AM, halim10-fes <halim10-fes@sust.edu> wrote:

> Dear Basil,
>
> Are you using any R package for your Analysis? For e.g.
> 'clustsig','PRIMER',
> etc. If you are using 'PRIMER', you can alternatively try using 'clustsig'
> and
> let us know what happened.
>
> Waiting eagerly to hear from you and others.
>
> P.S. Have you read the following article?
>
> CLARKE KR, SOMERFIELD PJ, GORLEY RN (2008) Exploratory null hypothesis
> testing for community data: similarity profiles and biota-environment
> linkage. J Exp Mar Biol Ecol 366, 56-69
>
>
> Best,
>
> ---------------
> Md. Abdul Halim
> Assistant Professor
> Department of Forestry and Environmental Science
> Shahjalal University of Science and Technology,Sylhet-3114,
> Bangladesh.
> Cell: +8801714078386.
> alt. e-mail: xou03@yahoo.com
>
>
>
> On Fri, 5 Jul 2013 18:37:33 -0500, Basil Iannone wrote
> > Dear R users,
> >
> > I am trying to conduct a simprof analysis to determine if groups of
> objects
> > form statistically significant clusters.
> >
> > The variables that I am using are a mixture of categorical, ordered,
> > and numerical. I am therefore using Gower's distance for this
> > analysis. Below is the code with my commentary.
> >
> > ### Below specifies the columns of the larger dataframe to use to
> calculate
> > ### distances among the objects in my dataset
> >
> > Fv<-F[,8:31]
> >
> > ### I feed the function below into the code for conducting simprof
> analyses
> > to
> > ###  specify what distance measure to use, i.e., to what
> "method.distance"
> > is ###  equal.
> >
> > G.Matrix <- function (Fv) FD::gowdis(Fv, ord = "metric")
> >
> > ### I then do the analysis.
> >
> > Fsp <- simprof(Fv, num.expected=1000, num.simulated=999,
> >                 method.cluster="average", method.distance=G.Matrix,
> >                 alpha = 0.01, silent=FALSE, increment=100)
> >
> > After that, I get the following error message:
> >
> >                    Error in FD::gowdis(Fv, ord = "metric") :
> >                      x is not a dataframe or a numeric matrix
> >
> > So it appears that the data used in a simprof analysis has to be numeric
> >
> > (which mine is not). The code structure does work when I use a dataframe
> > with purely numeric data. So my questions are:
> >
> > 1) Is there a way in R to run a Simprof analysis on data that is not
> > all numerical?
> >
> > 2) If not, why? That is, why can't simprof analyses be done on
> > non-numerical data. I read Clarke and Gorley's explanation in their
> PRIMER
> > manual of Simprof analyses and I was unclear from their description
> > as to why Simprof analyses cannot be conducted on non-numerical data.
> >
> > Finally, any suggested readings on the topic would be greatly
> appreciated.
> >
> > Thanks in advance for any assistance.
> >
> > Sincerely,
> >
> > --
> > Basil V. Iannone III
> > University of Illinois at Chicago
> > Department of Biological Sciences (MC 066)
> > 845 W. Taylor St.
> > Chicago, IL  60607-7060
> > Email: bianno2@uic.edu
> > Phone: 312-355-0987
> > Fax: 312-413-2435
> > http://www2.uic.edu/~bianno2
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> > --
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>
>
>
>
> --
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>


-- 
Basil V. Iannone III
University of Illinois at Chicago
Department of Biological Sciences (MC 066)
845 W. Taylor St.
Chicago, IL  60607-7060
Email: bianno2@uic.edu
Phone: 312-355-0987
Fax: 312-413-2435
http://www2.uic.edu/~bianno2

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