My objective is to look at differences in two species of fish from morphometric measurements. My morphometric measurements are head length, eye diameter, snout length, and measurements from tail to each fin. I want to use discrimanant function analyis to determine if there are differences between the two species. I am familiar with R but new to discrimannt function analysis. I want to learn how to run this analysis in R. My internet search has not been very successful. I did see refrence of the linear discriminant function (lda) in R but I am not sure if this is the correct function for me. Any advice and especially a reference to any examples would be greatly appreciated. Thanks. Mike [[alternative HTML version deleted]]
Hi, I did this exact thing for my masters, with intertidal fish, I just used a PCA? have you tried that? Sent from my iPhone On 16 Nov 2010, at 17:01, Mike Gibson <megalops31 at hotmail.com> wrote:> > My objective is to look at differences in two species of fish from morphometric measurements. My morphometric measurements are head length, eye diameter, snout length, and measurements from tail to each fin. I want to use discrimanant function analyis to determine if there are differences between the two species. > > I am familiar with R but new to discrimannt function analysis. I want to learn how to run this analysis in R. My internet search has not been very successful. I did see refrence of the linear discriminant function (lda) in R but I am not sure if this is the correct function for me. > > Any advice and especially a reference to any examples would be greatly appreciated. > > Thanks. > > Mike > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
On Tue, 2010-11-16 at 12:01 -0500, Mike Gibson wrote:> My objective is to look at differences in two species of fish from > morphometric measurements. My morphometric measurements are head > length, eye diameter, snout length, and measurements from tail to each > fin. I want to use discrimanant function analyis to determine if there > are differences between the two species. > > I am familiar with R but new to discrimannt function analysis. I want > to learn how to run this analysis in R. My internet search has not > been very successful. I did see refrence of the linear discriminant > function (lda) in R but I am not sure if this is the correct function > for me.With nothing further to go on, yes, use lda() in package MASS. It will find linear combinations of your morphometric variables that best discriminate between your two species of fish (i.e best separate the species).> Any advice and especially a reference to any examples would be greatly > appreciated.require(MASS) mod <- lda(Species ~ ., data = iris) mod plot(mod) plot(mod, dimen = 1) You might also be inclined to buy/track down this book: http://www.springer.com/statistics/life+sciences,+medicine+%26 +health/book/978-0-387-77789-4 which is in the UseR series from Springer on morphometric analysis using R. If you choose to buy, note that there is a 20% discount if you grab the code from the Books page on the R website and register with Springer. G> Thanks. > > Mike > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Hi, I am not sure if it is more robust than a discriminant function but it is certainly capable if differentiating between species based on morphology. I used 12 measurements in my fish. What did your PCA results show? Unfortunately I haven't got round to publishing my data yet but I can send you a paper by my supervisor who did a similar analysis looking at morphological differentiation in cichlids in Africa. Chris Sent from my iPhone On 25 Nov 2010, at 20:30, Mike Gibson <megalops31 at hotmail.com> wrote:> Sorry for the delay in getting back to you. > > I did use a PCA. > > I wanted to run a discriminant function as a comparison. Is PCA more robust at detecting differences based on the morphometrics? > > Can you give me the details of your masters (title, school, ect) so I can reference it. > > Mike > > > CC: r-help at r-project.org > > From: chrismcowen at me.com > > Subject: Re: [R] discriminant function analysis > > Date: Tue, 16 Nov 2010 22:12:32 +0000 > > To: megalops31 at hotmail.com > > > > Hi, > > > > I did this exact thing for my masters, with intertidal fish, I just used a PCA? have you tried that? > > > > Sent from my iPhone > > > > On 16 Nov 2010, at 17:01, Mike Gibson <megalops31 at hotmail.com> wrote: > > > > > > > > My objective is to look at differences in two species of fish from morphometric measurements. My morphometric measurements are head length, eye diameter, snout length, and measurements from tail to each fin. I want to use discrimanant function analyis to determine if there are differences between the two species. > > > > > > I am familiar with R but new to discrimannt function analysis. I want to learn how to run this analysis in R. My internet search has not been very successful. I did see refrence of the linear discriminant function (lda) in R but I am not sure if this is the correct function for me. > > > > > > Any advice and especially a reference to any examples would be greatly appreciated. > > > > > > Thanks. > > > > > > Mike > > > [[alternative HTML version deleted]] > > > > > > ______________________________________________ > > > R-help at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code.