Miranda,
The required inputs for gpagen do not change based on how you have organized
the data or how you collected it. From your description, it seems you have
incorrectly specified the input components.
First, the slide= option is for one to specify a ‘sliders’ matrix, in the style
used in TPSRelw (a m X 3 matrix specifying which landmarks are semilandmarks
and in which directions they should be slid). From your email you seem to have
this in a csv file, so read that into R and use this matrix.
Second, the 3D array of coordinates should contain the xy (or xyz) coordinates
of both the fixed points as well as the semilandmarks. They do not get input
separately, but in 1 matrix. In your case, since you seem to have the fixed
landmarks in one matrix and the semilandmarks in another, you will need to
concatenate these prior to performing gpagen.
Best,
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/http://www.public.iastate.edu/~dcadams/
phone: 515-294-3834
From: Karban, Miranda E [mailto:miranda-utzin...@uiowa.edu]
Sent: Wednesday, April 29, 2015 10:41 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] RE: Testing for sexual dimorphism
Dear Morphometricians,
I am attempting to upload 2D landmark and semi-landmark data into R (geomorph
package), and I was wondering if anyone could give me advice. In past analyses,
I have uploaded both a landmark tps file, which contains all of the landmark
and semi-landmark data combined (measured using tpsDig2), along with a sliders
csv file (made using tpsUtil), which indicates which points should be treated
as semi-landmarks. I am hoping to start using the draw background curves
(yellow pencil) tool in tpsDig2, which puts the curve information directly into
the landmark tps file. Does anyone know whether or not I need to indicate
within R that these curves exist? And if so, how?
I've tried using the following functon:
slide - as.matrix(read.tps(semilandmarks.tps))
but when I try to use the gpagen function:
procrustes - gpagen(landmarks, curves=slide, PrinAxes = FALSE)
the program crashes.
Thank you in advance for any help you can provide.
Best,
Miranda Karban
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