[R-sig-eco] Question about simprof

[halim10-fes]

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 at 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 at uic.edu
> Phone: 312-355-0987
> Fax: 312-413-2435
> http://www2.uic.edu/~bianno2
> 
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> 
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