-------- Original Message -------- Subject: Re: more CVA and LDF Date: Tue, 21 Oct 2008 16:15:48 -0200 From: Fabio de Andrade Machado <[EMAIL PROTECTED]> To: morphmet <[EMAIL PROTECTED]> References: <[EMAIL PROTECTED]> Hi again, YEah, I reading Claude's book and it is great and very versatile. I'm using the linear discriminant analysis function lda() for discrimination procedures as well as it seams simpler to classify individuals not included in the original analysis. Annat, the other function that I was referring was candisc(), of the candisc package (http://cran.r-project.org/web/packages/candisc/index.html). The help file kind of gives the impression that it refers to SAS's candisc function, but I not shure. cheers, Fabio Citando morphmet <[EMAIL PROTECTED]>:
-------- Original Message -------- Subject: Re: more CVA and LDF Date: Tue, 21 Oct 2008 07:44:43 -0700 (PDT) From: annat haber <[EMAIL PROTECTED]> To: [email protected] References: <[EMAIL PROTECTED]> Hi I just started using Claude's book "Morphometrics with R" and it's excellent. I wish it came out a year ago - would have saved me a lot of time and pain. It breaks down every procedure into the smallest functions, so it provides most of the basic codes you'd need but also leaves you enough room to practice writing your own in the way of combining them and incorporating data manipulation. I use lda for LDF/CVA, and it seems to work fine for any number of groups. the predict function gives you the posterior probabilities and allows you to test group membership for un-assigned specimens using the argument "newdata". So it's L <- lda(X, gr) pred<-predict(L) where X is a specimen-by-variable data matrix and gr is a vector specifying the grouping for each specimen in the same order that they appear in the matrix (so you don't need them to be sorted by groups in the data matrix and it can be any number of groups). The argument "method" allows you to specify which method is used. This will find either the dicriminant function (for two groups) or the canonical variates (for more than two groups). I don't know of another function in R for CVA/LDF - Fabio, which other function did you mean? If you meant the function cancor, that's for canonical correlations not canonical variates. Cheers, Annat ~~~~~~~~~ Annat Haber, PhD candidate Committee on Evolutionary Biology University of Chicago Culver Hall 402 1025 E. 57th St. Chicago IL 60637 Office: Hinds 289 c: 773 576 4205 http://home.uchicago.edu/~annat/ On Tue, Oct 21, 2008 at 7:08 AM, morphmet <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: -------- Original Message -------- Subject: Re: more CVA and LDF Date: Fri, 17 Oct 2008 18:15:15 -0700 (PDT) From: Paul Sanfilippo <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> To: [email protected] <mailto:[email protected]> References: <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> I'm also keen to hear any discussion about the differences between these two methods and also how to perform particularly a CVA in R. I've used the 'lda' function with cross-validation on a dataset which I think is giving me the information I want, but how do you perform a CVA, Fabio (or anyone else)? On a side note to R (which I've been using a bit lately and am findingI quite like, as steep as the learning curve is), has anyone read a book called 'Morphometrics with R' by Julien Claude? I'm mainly interested in learning how to use R to perform various statistical techniques once the data has been analysed with the various other GMM software, so I don't know how applicable this book is for me. Thanks, Paul Sanfilippo Uni Melbourne Australia On Fri, Oct 17, 2008 at 8:41 PM, morphmet <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: -------- Original Message -------- Subject: more CVA and LDF Date: Fri, 17 Oct 2008 01:59:31 -0700 (PDT) From: Fabio de Andrade Machado <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> To: [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> Hi all, Sorry to bring this up once more, but I don´t think any response on that have been posted (recently) on the list. What are the key differences of Canonical Variate Analysis and Linear Discriminant Functions? On Pete E. Lestrel´s "Morphometrics for the Life Science" it reads "A discriminant function is a linear equation, one per individual specimen, derived from the set of original variables x1, x2, x3, ...., xn, each of which is multiplied by a 'weighting' coefficient, a1,a2,a3,...,an (...). A set of these discriminant functions (...) is then computed for each individual case. Each discriminant function score is orthogonal with respect to all others". (p. 159-160) About Canonical Variate Analysis he says that it is design to calculate "[1](...) the correlation between two derived variables and [2] a set of canonical variates or canonical functions (as suns of weighted variables)(...)" (p.161). About both he says "Although displayed results are indistinguishable in many respects, the purpose are different" (p.160), being the CVA basically an graphical aid for LDF. Can anyone send some references on the specifics of each method? They seem distinct somehow. On R there are two different functions, being the one associated with CVA basically for graphical purposes (which is confusing, as the one can display graphically the results of discriminant functions and they seem basically the same). cheers, -- Fabio de Andrade Machado Laboratorio de Herpetologia/Morfometria Museu de Zoologia da USP Av. Nazaré, 481, Ipiranga São Paulo, SP, 04263-000 Brazil +55 11 61658120 +55 11 82631029 -- Replies will be sent to the list. For more information visit http://www.morphometrics.org <http://www.morphometrics.org/> -- Replies will be sent to the list. For more information visit http://www.morphometrics.org <http://www.morphometrics.org/> -- Annat Haber, Ph.D. candidate Committee on Evolutionary Biology University of Chicago 1025 E. 57th St. Culver Hall 402 Chicago IL 60637 [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> 773 576 4205 -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
-- Fabio de Andrade Machado Laboratorio de Herpetologia/Morfometria Museu de Zoologia da USP Av. Nazaré, 481, Ipiranga São Paulo, SP, 04263-000 Brazil +55 11 61658120 +55 11 82631029 -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
