RE: problem with fixed.angle?

[morphmet_moderator]

----- Forwarded message from "Adams, Dean [EEOBS]" <dcad...@iastate.edu> -----

Date: Sat, 20 Apr 2013 18:59:58 -0400
From: "Adams, Dean [EEOBS]" <dcad...@iastate.edu>
Reply-To: "Adams, Dean [EEOBS]" <dcad...@iastate.edu>
Subject: RE: problem with fixed.angle?
To: "morphmet@morphometrics.org" <morphmet@morphometrics.org>

Fabio,

I will investigate this issue.

Dean

--
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
Ames, Iowa
50011
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

---

From: morphmet_modera...@morphometrics.org [morphmet_modera...@morphometrics.org]
Sent: Friday, April 19, 2013 9:30 PM
To: morphmet@morphometrics.org
Subject: Re: problem with fixed.angle?

----- Forwarded message from Fabio Machado <macfa...@gmail.com> -----

Date: Fri, 19 Apr 2013 08:26:08 -0400
From: Fabio Machado <macfa...@gmail.com>
Reply-To: Fabio Machado <macfa...@gmail.com>
Subject: Re: problem with fixed.angle?
To: morphmet@morphometrics.org

I'm having an additional issue with fixed.angle after the previous correction: the configuration keeps rotating if I use the function another time. I'm not sure if the correction itself is doing this. If I use the function with the plethspecies data set, the modified function seems to work fine.

Any help is appreciated.

On 18/04/2013, at 21:52, Fabio Machado <macfa...@gmail.com> wrote:

Dear List,

I was trying to use the fixed.angle function in geomorph, and there seams to be a problem. The function deforms the resulting shape, even in the example given in the package. The problem seams to be in the centering on the rotation landmark, as you can check with the following code:

data(plethspecies)

plot(plethspecies$land[,,1],asp=1, xlim=c(-1,1))

points(plethspecies$land[,,1]-plethspecies$land[1,,1],asp=1, col="red")

fixed<-fixed.angle(plethspecies$land,art.pt=1,angle.pts=c(5,6),rot.pts=c(2,3,4,5))

points(fixed[,,1],asp=1, col="blue", pch=4)

Apparently, the subtraction of the articulation point follows "downwards" through the column and recycle through the entire configuration. I've altered the code of the function as following

A[, , i] <- A[, , i] - A[art.pt, , i]

to

A[, , i] <- t(t(A[, , i]) - A[art.pt, , i])

And this seams to solve the issue, but I'm not sure if I'm altering anything essential for the function or even if the problem I'm having is not due to anything else.

Any input is appreciated.

Best,

-----------------------------------------------------
Fabio Andrade Machado
Laboratório de Evolução de Mamíferos 
Departamento de Genética e Biologia Evolutiva
Universidade de São Paulo
Rua do Matão, trav.14, nº277, 

Edificio Minas Gerais 

05422-970
f.mach...@usp.br ; macfa...@gmail.com 

+55 11 3091-8758

+55 11 982-631-029

skype: fabio_a_machado

Lattes: http://lattes.cnpq.br/3673327633303737

Google Scholar: http://scholar.google.com/citations?hl=en&user=2l6-VrQAAAAJ

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