[R-sig-Geo] API documentation?

tom sgouros tomfool at as220.org
Tue Jul 1 04:30:29 CEST 2008 

Roger Bivand <Roger.Bivand at nhh.no> wrote:


> > I don't mean to rant, but believe me, I've spent plenty of time with
> > the documentation and it's really not helping.
> >
> > Partly this is a problem of R's doc format which treats package
> > documentation as an alphabetical list of functions - which gives me no
> > idea where to start.

I would tend to second this.  I've been lurking on the list for a few
months, hoping to learn a bit, but so far without much success, since
the conversation and the documentation are so far above where I am and
what I need.  I am almost familiar with R, using it for time-series
statistics, and learned early on that the Dalgaard book was a better
intro than any of the real R documents.  It doesn't cover nearly
everything, but it seems to cover what I needed, so I use what is
probably a baby-level set of R functions, but it's adequate.  Without a
professor lurking over my shoulder to explain stuff, I am perpetually
slightly lost, because all the documentation assumes I know stuff that I
don't.

I still use R because I know that with enough poking around it will
eventually provide a solution.  But if the alternatives were not very
expensive, I would have given up a while ago.

I joined this group when I wanted to expand into making maps of
geographical economic data, and after a month of working on the problem,
I essentially had to give up for the time being.  I wish there were an
introduction that showed me how to use R with a GIS program, but to my
knowledge, there is not.  I did run across a GRASS book that claimed it
would help, but as I recall, it cost upward of US$100.

To make this more useful than just a rant, I would second David's point.
What is missing is only what David misses: an introduction that says
where to start to deal with simple geographic data, maybe providing a
few examples of common techniques and frequent problems, and pushing
data back and forth to some GIS.  I was not able to find that, and
without it, found the R documentation pretty much useless.  I'd be happy
to know of some source I hadn't found before, so if you have one to
recommend, please do.

 -tom



> 
> This is an inherent (and perhaps ugly) characteristic of the S4
> object/class structure as you suggest below. New style classes are not
> as well integrated into the documentation as straight functions
> are. Here, coerce is as(), but the issue of how to improve
> documentation is not resolved.
> 
> >
> > This then interacts badly with the OO structure. For example, look at
> > the 20+ pages on "coerce". Hmm, what does "coerce" actually do? In
> > fact that's in a whole different library. But I didn't know that, so I
> > click on a page at random, say
> >
> > coerce,SpatialGrid,data.frame-method
> >
> > and this takes me to SpatialGrid class - which doesn't mention coerce
> > at all. (Nor does it tell me what SpatialGrid is, or what it is used
> > for.)
> >
> > On the other hand, maybe I might guess that to get a list of
> > coordinates, I'd use "coordinates". So I click on that method, and it
> > tells me yes, this "retrieves spatial coordinates". But unfortunately
> > it retrieves them hidden inside another object ("an object of class
> > SpatialPointsDataFrame"). OK, but how do I get the _actual_data_?
> > Maybe the SpatialPointsDataFrame class page will tell me. Nope. Et
> > cetera.
> >
> > Rick: yes, I agree that using the internal data structures is how to
> > do things, but this is broken isn't it? The whole point of having OO
> > is to be able to use it _without_ understanding the internal data
> > structures. The ideal, in other words, would be to have a "thin.lines"
> > method that I could just run on any polygon or set of polygons.
> > Failing that, then I should be able to get at the internal data
> > without hours of head scratching.
> >
> 
> No, because the underlying understanding of dp and other methods for
> thinning is that the objects implement an arc-node topological model,
> so that each arc can be thinned without different thinning happening
> on otherwise identical boundaries of neighbouring polygons. But we do
> not have an arc-node representation, so there cannot be line thinning
> for polygon boundaries in a spaghetti world.
> 
> > Right now, it's like, everything is hidden behind a layer of classes
> > and slots and methods, but I still need to go behind that layer to get
> > at the actual raw data, and this is so complicated and confusing that
> > it would be easier just to work with the raw data.
> >
> 
> You need to build topology first, so if need be take the data out to a
> GIS that does topology properly, do the arc line thinning there, and
> bring it back in. Building topology from a stream of straight line
> segments is a serious challenge, especially if you want to retain the
> association with attribute data.
> 
> Roger
> 
> > OK, I'll stop venting. If there's anything I could do to improve this
> > situation, I would gladly try.
> >
> > David Hugh-Jones
> > PhD Candidate
> > Essex University Department of Government
> > http://davidhughjones.googlepages.com
> >
> >
> > 2008/6/30 Virgilio Gomez-Rubio <v.gomezrubio at imperial.ac.uk>:
> >> Dear David,
> >>
> >> Probably the best way to start is by checking the HTML documentation. It
> >> should be installed locally but it is also accesible, for example, here:
> >>
> >> http://finzi.psych.upenn.edu/R/library/sp/html/00Index.html
> >>
> >> Hope this helps.
> >>
> >> Virgilio
> >>
> >> On Mon, 2008-06-30 at 18:48 +0200, David Hugh-Jones wrote:
> >>> Thanks David for his comment about dp.
> >>>
> >>> Quick question: is there any reasonably comprehensible API
> >>> documentation for the "sp" package? I have just spent about an hour
> >>> trying to get a list of points from a SpatialPolygons object. I
> >>> eventually just printed everything out and found the data by hand, so
> >>> now I am doing:
> >>>
> >>> coords <- myobject at polygons[[1]]@Polygons[[1]]@coords
> >>>
> >>> but I don't assume that is right. Surely there must be some simple way
> >>> to get a list of x and y coords out of any object?
> >>>
> >>> in frustration,
> >>> David Hugh-Jones
> >>> PhD Candidate
> >>> Essex University Department of Government
> >>> http://davidhughjones.googlepages.com
> >>>
> >>>
> >>> 2008/6/30 David PINAUD <pinaud at cebc.cnrs.fr>:
> >>>> maybe you can try the function dp() in the package "shapefiles", which is an
> >>>> implementation of the Douglas-Peucker polyLine simplification algorithm.
> >>>> Hope it helps
> >>>> David
> >>>>
> >>>> David Hugh-Jones a écrit :
> >>>>>
> >>>>> Hi all
> >>>>>
> >>>>> I have a big dataset of points and am doing stuff on them that takes a
> >>>>> lot of time. To speed it up, I would like to use "thinlines" from
> >>>>> RArcinfo, which basically makes the maps "rougher" by throwing away
> >>>>> points. Is there an equivalent function for SpatialPolygon type
> >>>>> objects? (I assume that there's no way to convert _to_ Arcinfo, though
> >>>>> I know it's possible to read from it).
> >>>>>
> >>>>> Cheers
> >>>>>
> >>>>> David Hugh-Jones
> >>>>> PhD Candidate
> >>>>> Essex University Department of Government
> >>>>> http://davidhughjones.googlepages.com
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-sig-Geo mailing list
> >>>>> R-sig-Geo at stat.math.ethz.ch
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> ***************************************************
> >>>> David PINAUD
> >>>> Ingénieur de Recherche "Analyses spatiales"
> >>>>
> >>>> Centre d'Etudes Biologiques de Chizé - CNRS UPR1934
> >>>> 79360 Villiers-en-Bois, France poste 485
> >>>> Tel: +33 (0)5.49.09.35.58
> >>>> Fax: +33 (0)5.49.09.65.26
> >>>> http://www.cebc.cnrs.fr/
> >>>>
> >>>> ***************************************************
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> ________ Information from NOD32 ________
> >>>> This message was checked by NOD32 Antivirus System for Linux Mail Servers.
> >>>> http://www.eset.com
> >>>
> >>> _______________________________________________
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> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> >>
> >
> > _______________________________________________
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> >
> 
> -- 
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at stat.math.ethz.ch
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