[R] discriminant function analysis

[Gavin Simpson]

On Thu, 2010-11-25 at 22:56 +0000, Chris Mcowen wrote:
> 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. 

PCA extracts linear combinations of the data that explain maximum
variance in the data, subject to the constraint that the sets of linear
combinations (the "axes") are uncorrelated (orthogonal).

LDA extracts linear combinations of the data that best separate the
group (species) means.

LDA would seem to be doing a more direct analysis if the question is how
can I differentiate my species in terms of their morphometrics.

G

> 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]]
> > > > 
> > > > ______________________________________________
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> > > > and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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