Jo,
There were two issues with the file. First, you had single curly quotes in
front of the specimen names. These should be simple ascii character quotes
instead.
Second, you had missing data in one of the specimens. For downstream analyses
in geomorph that is fine, but at present the read.morphologika function does
not handle these. The immediate solution is to replace these with -9999, then
read the file, and then replace them back to ‘NA’ within R. You can then
estimate the missing landmark locations using the ‘estimate.missing’ function
in geomorph, and continue with your other analyses.
Note that in the next version of geomorph we will add the ability to read
missing data directly from morphologika files, as is possible when reading TPS
files. Thank you for bringing this oversight to our attention!
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: Jo Gooding [mailto:jg1753.2...@my.bristol.ac.uk]
Sent: Monday, June 8, 2015 1:39 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] geomorph problem with morphologika file
Dear all,
I'm trying to read a morphologika formatted file into geomorph, but getting the
following error message:
> read.morphologika("combodatatest.txt")
Error in dimnames(coords)[[3]] <- names :
length of 'dimnames' [3] not equal to array extent
I'm not sure how I've formatted the .txt file incorrectly as it looks in
keeping with the geomorph manual example (my file is attached). Any suggestions
would be gratefully received!
Many thanks
Jo
--
Joanna Gooding
MSc Student
Palaeobiology and Biodiversity Research Group
School of Earth Sciences, University of Bristol
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