Hi Chris, I think I might have mis-spoken. What I really meant to say is that Matthew might want to consider doing a nested MANOVA, which, mathematically, is related to DA. I must confess that I've never done a nested discriminant analysis myself. Matthew said that he had considered doing this, so he might know. The data that I generally deal with do not exhibit multivariate normality, so DA and MANOVA are usually not appropriate options for me.
So, I have no idea which packages will do a nested DA. I know that the version of JMP (v.5) that I have cannot handle nested random effects when doing a MANOVA. It also doesn't allow you to define nested groups when doing DA. It's possible that SPSS and SAS can. I suspect that R can do it, since it apparently can do anything (if you know how to use it). Believe it or not, the old Macintosh program, SuperANOVA, which is easy as pie to use, but is now no longer produced (but could probably be purchased cheaply or borrowed), will allow you to do MANOVA with nested effects in the model. It will also provide eigenvectors, which can be used to calculate canonical scores and standardized canonical coefficients. One final point, if your data do not exhibit multivariate normality, then you might want to consider nonparametric MANOVA. McCune has made this available in the most recent version of PC ORD (v. 5). It will test nested effects, and it is very easy to use. It however will not provide anything analogous to canonical scores or standardized canonical coefficients. It tells you whether the nested effects and the group effects are statistically significant. It will also tell you which pairwise differences between groups are significant. Hope this helps some. Let me know if you want information about SuperAnova or PC-Ord. Steve At 7:31 PM -0500 8/21/06, Chris Taylor wrote: >Hey Steve. What do you run those nested discriminant analyses with? >Hope all is well! > >Chris > >At 11:18 AM 8/21/2006, you wrote: >>Matthew, >> >>You may also want to do a nested discriminant analysis to determine >>whether the mean morphology differs among populations, while >>controlling for species. The nesting of populations within species >>should "correct for phylogeny", unless there is something I'm missing >>here (e.g., phylogenetic relationships among populations within >>species). Don't really see the need for PICs. Make sure the >>assumptions of multivariate normality are met. >> >>Steve >> >> >> >> >> >> >>At 10:30 AM -0400 8/18/06, Matthew Gifford wrote: >>>I am looking for advice regarding principal components analysis. My >>>situation is as follows: I have a >>>data set of morphological measurements for 6 "taxa" (4 populations >>>of one species and 2 >>>populations of another). I read somewhere that in order to do a PCA >>>appropriately, one needs to >>>have more "taxa" (i.e., rows) than measurement variables (i.e., >>>columns). If I use mean values for >>>each "taxon" then I viiolate this assumption. To circumvent this, >>>is it valid to do a PCA on all data >>>and use mean PC scores? I will be using this information in >>>phylogenetically independent contrasts >>>analysis looking at ecomorphological relationships. Any >>>thoughts/opinions are most appreciated. >>> >>>Best, >>> >>>Matthew E. Gifford >>>Ph.D. Candidate >>>Washington University, St. Louis, MO >>>http://www.biology.wustl.edu/larsonlab/people/Gifford/Matt's_webpage.html >> >> >>-- >>Department of Biology >>PO Box 1848 >>University of Mississippi >>University, Mississippi 38677-1848 >> >>Brewer web page - http://home.olemiss.edu/~jbrewer/ >> >>FAX - 662-915-5144 >>Phone - 662-915-1077 > >*************************************************************** >Christopher M. Taylor >Associate Professor of Biological Sciences >Dept. of Biological Sciences >Mississippi State University >Mississippi State, MS 39762 >Phone: 662-325-8591 >Fax: 662-325-7939 >Email: [EMAIL PROTECTED] >http://www2.msstate.edu/~ctaylor/ctaylor.htm -- Department of Biology PO Box 1848 University of Mississippi University, Mississippi 38677-1848 Brewer web page - http://home.olemiss.edu/~jbrewer/ FAX - 662-915-5144 Phone - 662-915-1077
