----- Forwarded message from
morphmet_modera...@morphometrics.org -----
Date: Fri, 30 Nov 2012
14:11:31 -0800
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: RE: Problem
with MorphoJ and discriminant function
To:
morphmet@morphometrics.org
----- Forwarded message from
Débora Martínez
Date: Fri, 30
Nov 2012 04:57:20 -0500
From: Débora Martínez
Reply-To: Débora Martínez
Subject: RE: Problem with MorphoJ and
discriminant function
To:
morphmet@morphometrics.org
Thank you very muck Andrea,
How you say I think my problem is related with my data, since I work in 3D and I have a lot of landmarks, and the many iterations that the program has to perform for each comparison.
I will consider all your recommendations an I will try to do it as you have indicated me.
Best
Débora
How you say I think my problem is related with my data, since I work in 3D and I have a lot of landmarks, and the many iterations that the program has to perform for each comparison.
I will consider all your recommendations an I will try to do it as you have indicated me.
Best
Débora
> From:
morphmet_modera...@morphometrics.org
> To: morphmet@morphometrics.org
> Subject: Re: Problem with MorphoJ and discriminant function
> Date: Thu, 29 Nov 2012 22:31:47 -0800
>
>
> ----- Forwarded message from al cardini -----
>
> Date: Thu, 29 Nov 2012 04:56:01 -0500
> From: al cardini
> Reply-To: al cardini
> Subject: Re: Problem with MorphoJ and discriminant function
> To: morphmet@morphometrics.org
>
> Dear Débora,
> that's something that used to happen to me when I had many 3D
> landmarks. However, I guess it was simply taking its time for doing
> the resampling stats.
>
> I've noticed that since I installed the latest version, the software
> gets stuck every now and then (for instance, when saving a large
> project). I am not sure if that's OK or there's some kind of issue
> (possibly with java).
>
> For the permutation test and discriminant analysis, I am now doing
> those in R or in PAST using PCs of shape coordinates. If possible I
> use all of them, and that's the same as using all shape coordinates,
> or I select an appropriate number of the first PCs (enough for the
> change in pairwise shape distances to be minimal).
> This tends to work better, in my experience, and avoids some issues
> I've noticed a few times using shape coordinates. With appropriate N,
> results should be the same but if your N are small and/or
> heterogeneous across groups, things might become less straightforward
> (Evin et al., 2012, Journal of Archaeological Sciences, says something
> about this and has refs).
>
> For the visualization, especially with two groups, you could just do a
> PCA on the mean shapes of those two groups. PC1 will account for 100%
> of variance and you will be simply showing the mean shapes.
>
> In terms of ordinations, if you want to do a scatterplot summarizing
> group differences without distorting the spatial relationships in the
> Procrustes shape space (see Klingenberg & Monteiro, 2005, Syst.
> Biol.), you could also try the between group PCA (described in a few
> recent papers including Mitteroecker & Bookstein, 2011, and Seetah et
> al., 2012 - in my webpage with the full refs to the other papers I
> mentioned). BG-PCA is now implemented in PAST.
>
> Good luck.
> Cheers
>
> Andrea
>
> On 29 November 2012 09:09, <morphmet_modera...@morphometrics.org> wrote:
> >
> > ----- Forwarded message from Débora Martínez -----
> >
> > Date: Wed, 28 Nov 2012 09:50:17 -0500
> > From: Débora Martínez
> > Reply-To: Débora Martínez
> > Subject: Problem with MorphoJ and discriminant function
> > To: Morphmet
> >
> > Hello,
> >
> > I think I have a problem with MorphoJ and the discriminant function option.
> > When I try to perform this kind of analysis, my laptop takes a lot of time
> > to do it and I was only comparing two groups between them and not all the
> > pairwises. I have proved to perform the analyzes in another computers more
> > potent than mine and it is the same, the program is always running but I
> > cannot see the results. I also have proved with different MorphoJ versions
> > and it is also the same. Anyone can help me?? Anyone know what happens or if
> > I'm doing something wrong?
> >
> > Thanks in advance
> > Débora
> >
> >
> >
> > ----- End forwarded message -----
> >
> >
> >
>
> --
>
> NO DOCX, XLSX AND PPTX, PLEASE!!!
>
> COAUTHORS AND CONTRIBUTORS, PLEASE, FOR SHARING FILES, CONVERT THEM IN
> DOC, XLS (UNLESS LONGER THAN 256 COLUMNS) AND PPT
>
> Dr. Andrea Cardini
> Researcher in Animal Biology
> Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e
> Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
>
> Honorary Fellow
> Functional Morphology and Evolution Unit, Hull York Medical School
> University of Hull, Cottingham Road, Hull, HU6 7RX, UK
> University of York, Heslington, York YO10 5DD, UK
>
> Adjunct Associate Professor
> Centre for Forensic Science , The University of Western Australia
> 35 Stirling Highway, Crawley WA 6009, Australia
>
> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it,
> andrea.card...@hyms.ac.uk, andrea.card...@uwa.edu.au
>
> Webpage: http://sites.google.com/site/hymsfme/drandreacardini
> Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
> Editorial board for:
> Zoomorphology:
> http://www.springer.com/life+sciences/animal+sciences/journal/435
> Journal of Zoological Systematics and Evolutionary Research:
> http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
> Hystrix, the Italian Journal of Mammalogy:
> http://www.italian-journal-of-mammalogy.it/
>
> ----- End forwarded message -----
>
>
> To: morphmet@morphometrics.org
> Subject: Re: Problem with MorphoJ and discriminant function
> Date: Thu, 29 Nov 2012 22:31:47 -0800
>
>
> ----- Forwarded message from al cardini -----
>
> Date: Thu, 29 Nov 2012 04:56:01 -0500
> From: al cardini
> Reply-To: al cardini
> Subject: Re: Problem with MorphoJ and discriminant function
> To: morphmet@morphometrics.org
>
> Dear Débora,
> that's something that used to happen to me when I had many 3D
> landmarks. However, I guess it was simply taking its time for doing
> the resampling stats.
>
> I've noticed that since I installed the latest version, the software
> gets stuck every now and then (for instance, when saving a large
> project). I am not sure if that's OK or there's some kind of issue
> (possibly with java).
>
> For the permutation test and discriminant analysis, I am now doing
> those in R or in PAST using PCs of shape coordinates. If possible I
> use all of them, and that's the same as using all shape coordinates,
> or I select an appropriate number of the first PCs (enough for the
> change in pairwise shape distances to be minimal).
> This tends to work better, in my experience, and avoids some issues
> I've noticed a few times using shape coordinates. With appropriate N,
> results should be the same but if your N are small and/or
> heterogeneous across groups, things might become less straightforward
> (Evin et al., 2012, Journal of Archaeological Sciences, says something
> about this and has refs).
>
> For the visualization, especially with two groups, you could just do a
> PCA on the mean shapes of those two groups. PC1 will account for 100%
> of variance and you will be simply showing the mean shapes.
>
> In terms of ordinations, if you want to do a scatterplot summarizing
> group differences without distorting the spatial relationships in the
> Procrustes shape space (see Klingenberg & Monteiro, 2005, Syst.
> Biol.), you could also try the between group PCA (described in a few
> recent papers including Mitteroecker & Bookstein, 2011, and Seetah et
> al., 2012 - in my webpage with the full refs to the other papers I
> mentioned). BG-PCA is now implemented in PAST.
>
> Good luck.
> Cheers
>
> Andrea
>
> On 29 November 2012 09:09, <morphmet_modera...@morphometrics.org> wrote:
> >
> > ----- Forwarded message from Débora Martínez -----
> >
> > Date: Wed, 28 Nov 2012 09:50:17 -0500
> > From: Débora Martínez
> > Reply-To: Débora Martínez
> > Subject: Problem with MorphoJ and discriminant function
> > To: Morphmet
> >
> > Hello,
> >
> > I think I have a problem with MorphoJ and the discriminant function option.
> > When I try to perform this kind of analysis, my laptop takes a lot of time
> > to do it and I was only comparing two groups between them and not all the
> > pairwises. I have proved to perform the analyzes in another computers more
> > potent than mine and it is the same, the program is always running but I
> > cannot see the results. I also have proved with different MorphoJ versions
> > and it is also the same. Anyone can help me?? Anyone know what happens or if
> > I'm doing something wrong?
> >
> > Thanks in advance
> > Débora
> >
> >
> >
> > ----- End forwarded message -----
> >
> >
> >
>
> --
>
> NO DOCX, XLSX AND PPTX, PLEASE!!!
>
> COAUTHORS AND CONTRIBUTORS, PLEASE, FOR SHARING FILES, CONVERT THEM IN
> DOC, XLS (UNLESS LONGER THAN 256 COLUMNS) AND PPT
>
> Dr. Andrea Cardini
> Researcher in Animal Biology
> Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e
> Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
>
> Honorary Fellow
> Functional Morphology and Evolution Unit, Hull York Medical School
> University of Hull, Cottingham Road, Hull, HU6 7RX, UK
> University of York, Heslington, York YO10 5DD, UK
>
> Adjunct Associate Professor
> Centre for Forensic Science , The University of Western Australia
> 35 Stirling Highway, Crawley WA 6009, Australia
>
> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it,
> andrea.card...@hyms.ac.uk, andrea.card...@uwa.edu.au
>
> Webpage: http://sites.google.com/site/hymsfme/drandreacardini
> Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
> Editorial board for:
> Zoomorphology:
> http://www.springer.com/life+sciences/animal+sciences/journal/435
> Journal of Zoological Systematics and Evolutionary Research:
> http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
> Hystrix, the Italian Journal of Mammalogy:
> http://www.italian-journal-of-mammalogy.it/
>
> ----- End forwarded message -----
>
>
----- End forwarded message -----
----- End forwarded message
-----
