-------- Original Message --------
Subject: Re: CVA in MorphoJ vs LDA in R
Date: Mon, 13 Jul 2009 07:48:29 -0700 (PDT)
From: Dennis E. Slice <[email protected]>
To: [email protected]
References: <[email protected]>
Cross-checking with multiple programs is a good idea, as is knowing and
understanding what a particular program is doing. I, myself, check the
results of all of my software against other programs that should provide
similar results and/or recode all in R. Note the latter does not
preclude a logic error in which the wrong thing is computed correctly in
two or more programs.
Best, ds
morphmet wrote:
-------- Original Message --------
Subject: RE: CVA in MorphoJ vs LDA in R
Date: Mon, 13 Jul 2009 03:09:36 -0700 (PDT)
From: Louis Boell <[email protected]>
To: <[email protected]>, <[email protected]>
References: <[email protected]>
<c67cb266.6feb%[email protected]>
Hi Annat,
No, I didn´t receive any answer. I guess that there are not many people
who know enough about both programs to provide the solution.
What I find troublesome in this respect is that your results seem to
depend sometimes from the software you are using. When the software is
intransparent, and you don´t care how it works, and you try only one
program, you might easily end up drawing malinformed conclusions (I
obtained even more bizarre results in SPSS, with most of the CV axes
being identical to those in MorphoJ and four axes being different!).
The only solution I can see for my problem is to try and implement,
e.g., the very same procedure used by MorphoJ in R so that I understand
how it works exactly. I have 13 groups (or even more in some of the
analyses). I hope that I will be able to solve this problem. I expect to
learn a lot while trying! ;-)
Best wishes,
Louis
Louis Boell
MPI für Evolutionsbiologie
August-Thienemannstr.2
24306 Plön
[email protected]
[email protected]
> Date: Fri, 10 Jul 2009 08:55:02 -0500
> Subject: Re: CVA in MorphoJ vs LDA in R
> From: [email protected]
> To: [email protected]
>
> Hi Louis,
> Did you get an answer to your question yet?
> I had a similar problem a while ago and I noticed that if I use the
whole
> configuration I get less separation between the groups then if I use
half of
> it - I'm working with bilateral symmetric objects (skulls) and use
only the
> symmetric component so the two halves are redundant. I didn't
investigate it
> in depth yet, but seems like the redundancy decreases the separation for
> some reason (I don't know enough linear algebra to say why...).
> How many groups do you have btw? The mathematical procedure is
different if
> you have two groups or more. It's a simple calculation in the case of
2 but
> there are several ways for determining the CV's in the case of more
than 2,
> at least in R, so that might be difference between the two softwares
(I only
> had 2).
> I hope that helps somewhat. In any case, I'd be interested to know
what is
> the solution to this.
>
> Best,
> Annat
>
> > From: morphmet <[email protected]>
> > Reply-To: <[email protected]>
> > Date: Tue, 07 Jul 2009 10:06:41 -0400
> > To: morphmet <[email protected]>
> > Subject: CVA in MorphoJ vs LDA in R
> > Resent-From: <[email protected]>
> > Resent-Date: Tue, 7 Jul 2009 07:08:51 -0700 (PDT)
> >
> >
> >
> > -------- Original Message --------
> > Subject: CVA in MorphoJ vs LDA in R
> > Date: Mon, 6 Jul 2009 08:34:07 -0700 (PDT)
> > From: Louis Boell <[email protected]>
> > To: <[email protected]>
> >
> >
> >
> > Dear colleagues,
> >
> > I encountered the following problem: in R, I performed least
> > discriminant analysis (lda) using as the argument Procrustes
coordinates
> > calculated by procGPA . I then used the "predict" function to
calculate
> > Mahalanobis distances between groups. I was, however, surprised to see
> > that the resulting Mahalanobis distances between groups do
fundamentally
> > differ from those calculated using CVA in MorphoJ, based on the
same set
> > of procrustes distances also calculated in R.
> > I had thought that LDA was close to being identical to CVA and had
thus
> > expected very similar results. Did I omit an important step? As far
as I
> > know, the procGPA coordinates have already been projected in the
tangent
> > space, and first calculating a PCA and omitting the last four scores
> > should not much affect the results.
> > I have rechecked both my Procrustes coordinates and the grouping
factor.
> > Everything seems fine.
> > Is there solmething fundamental I might be ignoring?
> > Thanks for advice, best wishes
> >
> > Louis Boell
> >
> >
> >
> > Louis Boell
> > MPI für Evolutionsbiologie
> > August-Thienemannstr.2
> > 24306 Plön
> > [email protected]
> > [email protected]
> >
> >
> >
> >
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> > For more information visit http://www.morphometrics.org
> >
>
>
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