RE: tps format problem reading in R

[morphmet]

-------- Original Message --------
Subject: RE: tps format problem reading in R
Date: Wed, 3 Jul 2013 11:32:55 -0400
From: Adams, Dean [EEOBS] <dcad...@iastate.edu>
To: morphmet@morphometrics.org <morphmet@morphometrics.org>

Hi John,



ID <-sub("ID=", "", tpsfile[grep("ID", tpsfile)])   #delete the 'as.numeric'
dimnames(coords)[[3]] <- as.list(imageID)   # add 'as.list'




Thanks for catching these; this makes the function more general.

Best,

Dean

--
Dr. Dean C. Adams
Professor

50011
www.public.iastate.edu/~dcadams/
phone: 515-294-3834


-----Original Message-----

There were two issues here, and both of which have easy fixes. First, there is only 1 specimen in your tps file, and the current version of readland.tps() was written for datasets with more than one specimen (we didn't envision folks reading in a single specimen for a morphometric analysis). This is easily fixed by changing the 3rd to last line of the function as below. Next, your file had a non-numeric ID for the specimen. To catch this, change the 4th to last line of the function as below. These two lines should now read: The updated function code is attached, and will be in the next update of geomorph. Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University Ames, Iowa From: morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org]

Sent: Wednesday, July 03, 2013 1:31 AM
To: morphmet@morphometrics.org
Subject: tps format problem reading in R


----- Forwarded message from John Denton <jden...@amnh.org> -----

     Date: Tue, 2 Jul 2013 23:04:22 -0400
      From: John Denton <jden...@amnh.org>
      Reply-To: John Denton <jden...@amnh.org>
      Subject: tps format problem reading in R
      To: "morphmet@morphometrics.org" <morphmet@morphometrics.org>

Hi folks,

I'm trying to read a tps file in the geomorph v1.1-1 R package using

readland.tps("file"),

but every time I try the above, I get the error


In readland.tps("Lter_mean.TPS") : NAs introduced by coercion





The file is attached.

~John

John S. S. Denton
Ph.D. Candidate


----- End forwarded message -----

Error in dimnames(coords)[[3]] <- imageID : 'dimnames' must be a list In addition: Warning message: I do not get the error when I read in some of my other tps files (all of which were produced using append files in tpsUtil). The file I'm trying to read in is the side-averaged Procrustes coordinates, generated in MorphoJ. I've checked the hidden formatting, the line breaks, the number of decimal places, and the file extension, but I can't seem to figure it out. Department of Ichthyology and Richard Gilder Graduate School American Museum of Natural History www.johnssdenton.com

readland.tps
Description: Binary data