Hi Basil, Sandra Pavoine has a nice R script for dealing with different data types in the same analysis, which creates a dissimilarity matrix that can be input directly into FD: http://goo.gl/C9jUM
Dylan On Sat, Jul 6, 2013 at 12:08 PM, Basil Iannone <bian...@uic.edu> wrote: > 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-...@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: xo...@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: bian...@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 > > > > > > -- > > > This message has been scanned for viruses and > > > dangerous content by MailScanner, and is > > > believed to be clean. > > > > > > > > > > -- > > This message has been scanned for viruses and > > dangerous content by MailScanner, and is > > believed to be clean. > > > > > > > -- > Basil V. Iannone III > University of Illinois at Chicago > Department of Biological Sciences (MC 066) > 845 W. Taylor St. > Chicago, IL 60607-7060 > Email: bian...@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 > -- Dylan J. Craven, M.F.S., Ph.D. Post-Doctoral Fellow Universite du Quebec a Montreal E-mail: dylan.cra...@aya.yale.edu Personal Website: dylancraven.weebly.com Skype: elgringacho [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
