[GRASS-dev] R and GRASS integration

[Paulo van Breugel]

On Wed, Jan 6, 2016 at 10:27 AM, Rainer M Krug <Rainer at krugs.de> wrote:

> Paulo van Breugel <p.vanbreugel at gmail.com> writes:
>
> > I by any stretch of imagination a developer, but I did use the
> > combination of shell or pythons script with R, basically following the
> > approach you described, having a python or shell script write a R
> > script to a text file and run it. I think it can work well, and not
> > that much harder to maintain. But I also would be very interested to
> > learn how to do this better. I also would be interested to see the
> > randomForest scripts you mentioned Steven, are you already sharing it
> > somewhere?
> >
> > As you mentioned, there are probably many people using / writing R
> > scripts that interact with GRASS. For some it will be easier, or it
> > may be more logical for them, to turn these into R packages rather
> > than writing a GRASS addon.
>
> I am one of those. I have thought about making a GRASS (or QGIS) addon /
> plugin, but I stayed with the R package. I have a complete simulation
> written in R which uses spatial data from GRASS, does simulations, and
> returns the results to GRASS.
>

> To run the simulations in itself is a three liner in R.
>
> > It would be nice if there would be some kind of repository where
> > people share such code (github perhaps?). I am sure there are existing
> > ones on e.g., github, so perhaps just a GRASS-wiki page listing
> > existing repositories would be enough. I know there is
> > https://grasswiki.osgeo.org/wiki/R_statistics, but I don't think there
> > is an place on the GRASS website, wiki or trac to share/list R code?
> > Would this be of interest to create such page (on the Wiki perhaps?).
>
> Different people use different repos (I use e.g. github and gitlab) so
> creating another place where I should publish my code would be not
> really an option. What would be an idea to make it easy (probably even
> easier even than editing a wiki page?) to add a repo to a list of
> projects which integrate R in GRASS or GRASS in R, and which could
> indicate the last commit to aser if the repos are current or just
> archives from e.g. papers or finished projects.
>

+1 That would be something quick to implement. However, what form did you
have in mind, if not a wiki page? I wouldn't mind creating such page, but
perhaps first some further ideas on the best form from others as well.

>
> My repo is private at the moment, but I plan to make it open in the next
> few weeks.
>
> A brief presentation about a very similar simulation model can be
> found at
>
> https://github.com/rkrug/INTECOL_2013_Optimizing
>
>
> Thanks for sharing, interesting. Looking forwards seeing some further code


>
> My gitlab repos (most or all private at the moment) are at
>
> https://gitlab.com/rkrug/asm
>
> and the simulation is at (also still private but it will change soon)
>
> https://gitlab.com/rkrug/asm
>
> For reference, my github page is at
>
> https://github.com/rkrug
>
> Cheers,
>
> Rainer
>
>
> >
> > Paulo
> >
> >
> > On 04-01-16 16:14, Steven Pawley wrote:
> >> Thank you Moritz,
> >>
> >> Yes I have also had difficulties with Rpy2 apart from on
> >> Linux. Also, Rpy2 is quite onerous in terms of effort required to
> >> integrate R scripts into Python. Your solution certainly works, but
> >> as you mentioned it makes the R script harder to maintain. PypeR is
> >> another alternative and is straightforward to install and is simpler
> >> from a user perspective.
> >>
> >> I would also be interested in hearing opinions from 'true'
> >> developers who have much greater expertise than myself in this area.
> >>
> >> Kind regards,
> >>
> >> Steve
> >>
> >>> On Jan 4, 2016, at 2:31 AM, Moritz Lennert <
> mlennert at club.worldonline.be> wrote:
> >>>
> >>>> On 04/01/16 10:28, Moritz Lennert wrote:
> >>>>> On 03/01/16 23:54, Steven Pawley wrote:
> >>>>> Like many R-GRASS users, I have a collection of R scripts that
> >>>>> interact with GRASS to perform various workflows. I have debated
> >>>>> about converting these to Python using Rpy2, although this package
> >>>>> can be a difficult to install on all platforms and depends on
> >>>>> specific versions of R and Python. I noticed that Moritz Lennert
> >>>>> recently developed a GRASS add on which consists of simply writing
> >>>>> out the R commands to a temporary script for R to run.
> >>>> [...]
> >>>>> Does this represent a desirable or even acceptable approach for
> >>>>> embedding R scripts into grass add ons, or is Rpy2 the 'official'
> >>>>> approach.
> >>>> I wouldn't consider my approach in any way official, but AFAIK, rpy2
> >>>> does not have any "official" status in GRASS either. In my particular
> >>>> case (v.class.mlR) this was a quick and dirty hack for a course I had
> to
> >>>> teach. The difficulty of getting rpy2 installed on the lab machines on
> >>>> short notice was one of the motivations not to use it. I also agree
> that
> >>>> dependency on rpy2 can be a nuisance and has caused me some headaches
> >>>> with other modules, before. However, the approach I used (and others
> >>>> have used before) is a bit unwieldy and makes maintaining such
> modules a
> >>>> bit of a pain.
> >>>>
> >>>> So, I'm curious to hear the opinions of others...
> >>> See [1] for a related issue.
> >>>
> >>> Moritz
> >>>
> >>> [1] https://trac.osgeo.org/grass/ticket/1290
> >> _______________________________________________
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> >
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>
> --
> Rainer M. Krug
> email: Rainer<at>krugs<dot>de
> PGP: 0x0F52F982
>
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