basic, starter questions on geomorph

[Shott,Michael]

Dear Emma,

I’ve used GM sporadically on archaeological data—chipped stone tools.  I’m no more than ordinarily obtuse.  However, in the process of trying to learn geomorph I encounter fundamental problems at the outset. 

 

Please forgive these extremely basic questions but, frankly, your documentation seems, upon my first reading of essential passages, to assume a great deal that it fails to specify in its 139-pp and that new users may not know.  At least this one doesn’t.

 

I’ve downloaded geomorph, and completed all of pg. 10’s steps.  OK, geomorph works in R.  But let’s move to my own data.  I’m starting from a set of already-digitized 3D LMs and semiLMs for a set of tools, received as a .csv file.  That’s likely a problem, but it’s easy enough to save files under other extensions.  If I read correctly your Sec. 1.6, pp 11-12, it’s a 2D array of 3D data.  But first things first, because I haven’t gotten far enough to find that out.  Instead, I’ve foundered on two more immediate problems:

1.       Exactly what file types does geomorph accept?  Rather than listing a few of the more common ones, pg. 16 refers me to Rohlf 2012.  That’s a commercial document/app that I’m unwilling to spend money on just to find out if .xls or .txt files are acceptable.  Rohlf’s site may provide the Googling the question didn’t help; it rarely does if one doesn’t have three hours or so to wade through oceans of irrelevant sites.  Checking your document again, Sec. 2, top of pg. 15 discusses “At the end” how to import data “as a simple excel-style matrix”.  Reading all of Sec. 2 line-by-line through pg. 21, I never again encountered the word “excel.”  But Sec. 2.4 (pg. 20) seems to be “the end” to which the starting paragraph refers, and it speaks of .txt files.  So, is there instead a simple list of file types that geomorph will accept?

2.       Assuming the problem 1 is solved (pretty basic; let’s hope so), pg. 20 (Sec. 2.4) advises me on how to read in data that aren’t .nts etc.  Useful, sincerely.  But exactly where do I read them in from?  Your “filelist” example tells me that it lists all files “in working directory”.  What is the working directory?  Where is it? How can I copy files held on my dept.’s server to it or read them into it for subsequent reading via filelist?  Can I specify the full path (e.g., “<-read.table (“Q:/…myfile.extension”, header=TRUE, row.names=1…”strings etc.?  If so, OK.  But if that won’t work, there must be some simple way to access files held on C:/ drives or servers in either geomorph or R, then to somehow place them in whatever the “working directory” is so that they can be identified by filename only.  Apologies, but an hour or more of reading sections of your guide didn’t answer that simple question for me.

 

I also consulted the geomorph wiki which also, frankly, seems unhelpful.  I’m already apprehensive because at the very start I encounter problems with the most fundamental matters.  It’s as though I bought a new car and received the dealer’s advice to use my key/fob to open and start it, without being given the key/fob or told where the car is.

 

Hoping you can help,

MS

Michael Shott

Prof., Dept. of Anthropology & Classical Studies

Univ. of Akron

Akron, OH 44325 USA

+01(330)972-6890

 

[Adams, Dean [EEOBS]]

Michael,

 

Your issues are in a lack of basic understanding of how to input data into R; it is not an issue with geomorph, its help files, or its manual.

 

First, geomorph does not ‘accept’ any excel format: R does. R also accepts text files, binary files, and other formats.  Second, it is R which requires the user specify in what directory one’s data files may be found (R is not a point-and-click gui package: it is command line, and command line programs require this sort of specification).  As such, it is the user that must learn sufficient R-skills to know how to do this and to bring their data into R.  Once that has been successfully completed, the functions we provide in geomorph allow one to convert the data matrix into an object the analytical functions will be able to recognize.

 

It is simply unreasonable to think it within the purview of geomorph’s authors to provide basic R skills, along with a package that performs proper morphometric analyses of such data. Likewise, it is incorrect to assume it a ‘failing’ of geomorph when someone cannot bring their data into R. 

We happily provide geomorph to the scientific community and do so freely, but one must recognize that we do this as a volunteer service of our time. If one is not satisfied with how the program functions, then one is free to use other available software, or write their own. 

 

Dean and the geomorph team

 

Dr. Dean C. Adams

Director of Graduate Education, EEB Program

Professor

Department of Ecology, Evolution, and Organismal Biology

       Department of Statistics

Iowa State University

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

--
You received this message because you are subscribed to the Google Groups "geomorph R package" group.
To unsubscribe from this group and stop receiving emails from it, send an email to geomorph-r-pack...@googlegroups.com.
To post to this group, send email to geomorph-...@googlegroups.com.
Visit this group at https://groups.google.com/group/geomorph-r-package.
To view this discussion on the web, visit https://groups.google.com/d/msgid/geomorph-r-package/DM5PR07MB3596DCE3E75B77632F5264B3D8FD0%40DM5PR07MB3596.namprd07.prod.outlook.com.
For more options, visit https://groups.google.com/d/optout.