Dear ALL, The geomorph R package uses the very flexible list data structure in R to store and retrieve morphometric datasets consisting of landmark coordinates, interlandmark links, classification factors, and outlines. This is simple enough, but I have a number of doubts arising from my attempts at reading data files in TPS format with geomorph readland.tps() function.
Specifically, I have not been able to read any of the sample files sneathd.tps, Fig517.tps and Fig518.tps provided with Jim Rohlf's tpsSplin program. These files do not seem to adhere to the most strict TPS format adopted by geomorph - so, instead of using an "ID" field, these files simply put the specimen identification in the file header (for example, LM=25 Fig517). The tps series of programs are seemingly more liberal than the geomorph package when handling TPS. I then manually adjusted this, creating an ID field and removing all extra information not handled by geomorph, and in this way I have managed to read the file in geomorph using fig517 <- readland.tps(file="fig517.tps", specID = "ID", readcurves=TRUE)... well, more or less! The resulting object is a messy matrix with NA values mixed with landmark and outline coordinate data, of which I could not make any sense. So, my general question is: how to get landmark *and* outline data from a TPS file read correctly in geomorph? Alternatively, could I read the outlines as a simple two-dimensional matrix, merging all the curves (as it seems to be the case of the outlines in the plethodon sample dataset provided with geomorph)? For convenience, I attach the sample fig517.tps (fixed as fig517a.tps) file to this message. Thanks in advance for any assistance you can provide. With *best* wishes, -- Dr. Mauro J. Cavalcanti E-mail: [email protected] Web: http://sites.google.com/site/maurobio "Life is complex. It consists of real and imaginary parts." -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CAC1JhZaqtZx%3DvHSVy84rOS_KeOoKqa7OO%2BXs3Z7UJuYWLW3TWw%40mail.gmail.com.
fig517a.tps
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