Dear Jim,
Nothing to be sorry about! In fact, the way TPS files were structured was
very flexible, although surely an adherence to the defined fields ('ID',
'CURVES', 'POINTS', etc.) is required for consistency and making the files
readable by other software.
Anyway, my intention is to be able to read these 'old' TPS files (properly
'fixed') with geomorph and reproduce the figures for a book I am (slowly)
working on. Hope some of the amazing R wizards here can help me.
With *best* wishes,
Em qui., 6 de ago. de 2020 às 19:42, [email protected] <
[email protected]> escreveu:
> Oops! You are correct about the "illegal" structure of those two files. I
> should at least follow my own rules! I have just corrected those two files
> so future downloads will be correct once I upload the corrected version. My
> only excuse is that they were created a long time ago as the tpsSplin
> programs was the first to be distributed.
>
> Sorry for causing a problem - and thanks for reporting it.
>
> *F. James Rohlf *
> Distinguished Professor, Emeritus
> Depts: Anthropology and Ecology & Evolution
> Stony Brook University
>
> On 8/6/2020 11:59:06 AM, Mauro Cavalcanti <[email protected]> wrote:
> 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."
>
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>
>
--
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."
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