[R-sig-Geo] 4. R from cgi and Xvfb (G. Allegri)
G. Allegri
giohappy at gmail.com
Thu Jan 17 15:50:06 CET 2008
I've solved using Cairo library. For now it's enough, then I'll try to
solve with Xvfb solution...
Thanks to all!
Giovanni
2008/1/16, G. Allegri <giohappy at gmail.com>:
> I've tried using bitmap(), but it returns this taceback:
>
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] GPL Ghostscript
> SVN PRE-RELEASE
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] 8.61
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] :
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] **** Could not
> open the file prova.png .
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] GPL Ghostscript
> SVN PRE-RELEASE
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] 8.61
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] :
> [Wed Jan 16 16:10:05 2008] [error] [client 127.0.0.1] Unrecoverable
> error, exit code 1
>
> I think ghostscript is trying to access the postcript file, but isn't
> able. It works perfectly out of Apache...
>
> I try with Cairo... my last try!
>
> 2008/1/16, Paul Hiemstra <p.hiemstra at geo.uu.nl>:
> > Hi Giovanni,
> >
> > You could consider using 'bitmap()' instead of png(). I seem to remember
> > that the first uses postscript devices and does not need X11. Another
> > options would be to use the Cairo package, 'Cairo' initializes a new
> > graphics device that uses the cairo graphics library for rendering. See
> > ?bitmap and ?Cairo.
> >
> > Hope this helps,
> >
> > Paul
> >
> > G. Allegri wrote:
> > > Thanks Marcelo,
> > > I've tried using the suexec module in apache2 (it permits to change
> > > userid and groupid on the base of the scripts called), but from
> > > documentation appears to work only for CGI and SSI, not with
> > > mod_python.
> > > So, I change mailing-list, since the problem is almost OT now in this one :-)
> > >
> > > Giovanni
> > >
> > > 2008/1/16, Marcelo Oliveira <moliveira at geostats.com>:
> > >
> > >> Giovanni,
> > >>
> > >> This issue could be related to user permissions. See if you can get
> > >> Apache running under a user with display access rights.
> > >>
> > >> Good Luck,
> > >>
> > >> Marcelo
> > >>
> > >> -----Original Message-----
> > >> From: r-sig-geo-bounces at stat.math.ethz.ch
> > >> [mailto:r-sig-geo-bounces at stat.math.ethz.ch] On Behalf Of
> > >> r-sig-geo-request at stat.math.ethz.ch
> > >> Sent: Wednesday, January 16, 2008 6:00 AM
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Subject: R-sig-Geo Digest, Vol 53, Issue 14
> > >>
> > >> Send R-sig-Geo mailing list submissions to
> > >> r-sig-geo at stat.math.ethz.ch
> > >>
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> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >> or, via email, send a message with subject or body 'help' to
> > >> r-sig-geo-request at stat.math.ethz.ch
> > >>
> > >> You can reach the person managing the list at
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> > >>
> > >> When replying, please edit your Subject line so it is more specific
> > >> than "Re: Contents of R-sig-Geo digest..."
> > >>
> > >>
> > >> Today's Topics:
> > >>
> > >> 1. Re: Spatially Constrained Clustering (Elias T. Krainski)
> > >> 2. regression kriging in gstat with skewed distributions (G. Allegri)
> > >> 3. I Would Dream (vacates at patiencegroup.com)
> > >> 4. R from cgi and Xvfb (G. Allegri)
> > >> 5. Re: regression kriging in gstat with skewed distributions
> > >> (Tomislav Hengl)
> > >>
> > >>
> > >> ----------------------------------------------------------------------
> > >>
> > >> Message: 1
> > >> Date: Tue, 15 Jan 2008 10:51:48 -0300 (ART)
> > >> From: "Elias T. Krainski" <eliaskrainski at yahoo.com.br>
> > >> Subject: Re: [R-sig-Geo] Spatially Constrained Clustering
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Message-ID: <569895.79461.qm at web50604.mail.re2.yahoo.com>
> > >> Content-Type: text/plain; charset=iso-8859-1
> > >>
> > >> Hello Carson,
> > >>
> > >> See the SKATER software at
> > >> http://www.est.ufmg.br/leste/skater.htm
> > >> The SKATER is a Spatial 'K'luster Analisys by Tree
> > >> Edge Removal. In future, this method also be available
> > >> in R.
> > >>
> > >> Best,
> > >> Elias.
> > >>
> > >> --- Carson Farmer <cfarmer at uvic.ca> escreveu:
> > >>
> > >>
> > >>> Hello List,
> > >>>
> > >>> I am trying to find an R package that will
> > >>> accommodate spatially
> > >>> constrained clustering. While I have been unable to
> > >>> find a package that
> > >>> is explicitly designed to do spatially constrained
> > >>> clustering, I was
> > >>> wondering if anyone had found a package that would
> > >>> do constrained
> > >>> clustering of any kind, and adapted this to spatial
> > >>> constraints?
> > >>> I have searched the R site extensively, and googled
> > >>> all night long, but
> > >>> to no avail! I HAVE found this post:
> > >>>
> > >>>
> > >> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/56819.html
> > >>
> > >>> but the replies did not help much. They lead to
> > >>> several packages which
> > >>> perform spatial clustering (such that significant
> > >>> clusters of say a
> > >>> disease are located within a study region), however,
> > >>> what I would like
> > >>> to do is partition a spatial (grid) dataset based on
> > >>> multiple variables,
> > >>> taking into account their spatial locations (i.e.
> > >>> clustering is based on
> > >>> the variables, but constrained so that clusters are
> > >>> spatially
> > >>> contiguous). I'm thinking mclust is probably the
> > >>> best way to go, but
> > >>> I'm not sure where to start.
> > >>>
> > >>> Any suggestions would be greatly appreciated.
> > >>>
> > >>> Thanks,
> > >>>
> > >>> Carson
> > >>>
> > >>> _______________________________________________
> > >>> R-sig-Geo mailing list
> > >>> R-sig-Geo at stat.math.ethz.ch
> > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >>>
> > >>>
> > >> Elias T. Krainski
> > >>
> > >>
> > >>
> > >> ------------------------------
> > >>
> > >> Message: 2
> > >> Date: Tue, 15 Jan 2008 15:27:58 +0100
> > >> From: "G. Allegri" <giohappy at gmail.com>
> > >> Subject: [R-sig-Geo] regression kriging in gstat with skewed
> > >> distributions
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Message-ID:
> > >> <e12429640801150627q7266a599g77a3df9744edb153 at mail.gmail.com>
> > >> Content-Type: text/plain; charset=WINDOWS-1252
> > >>
> > >> I'm trying to realize e regression kriging with gstat package on my
> > >> soil samples data. The response variable (ECe measuere) and covariates
> > >> appear positvely skewed.
> > >> As Tomislav Hengl suggests in its "framework for RK" [1], a logistic
> > >> transformation is proposed as a generic way to reduce the skeweness by
> > >> using the physical limits of the data.
> > >> Is it really a transformation that can be applied in the generic case
> > >> of skewed datas? I mean,in my case I have non-normal residuals (from
> > >> original data regression), and I'm trying to transform the residuals
> > >> (and not the original values) to do SK on them . Is this approach
> > >> correct?
> > >>
> > >> A related question is how to do normal score transformations (for my
> > >> residuals) in R and gstat. I know gstat doesn't manage transformations
> > >> and back-transformations, so it should be done previously in R... but
> > >> I can't find any package that permit it in a straisghtforward way.
> > >> I've found something with qqnorm(ppoints(data)) and the approx()
> > >> function. Is that all?
> > >>
> > >> Giovanni
> > >>
> > >>
> > >> [1] "A generic framework for spatial prediction of soil variables
> > >> based on regressionkriging" Geoderma 122 (1?2), 75?93.
> > >>
> > >>
> > >>
> > >> ------------------------------
> > >>
> > >> Message: 3
> > >> Date: Tue, 15 Jan 2008 19:25:16 +0100
> > >> From: <vacates at patiencegroup.com>
> > >> Subject: [R-sig-Geo] I Would Dream
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Message-ID: <478CFA8C.7030508 at patiencegroup.com>
> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > >>
> > >> Kisses Through E-mail http://86.123.21.76/
> > >>
> > >>
> > >>
> > >> ------------------------------
> > >>
> > >> Message: 4
> > >> Date: Wed, 16 Jan 2008 11:04:53 +0100
> > >> From: "G. Allegri" <giohappy at gmail.com>
> > >> Subject: [R-sig-Geo] R from cgi and Xvfb
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Message-ID:
> > >> <e12429640801160204h3532ddb9t624b4f6ef658c975 at mail.gmail.com>
> > >> Content-Type: text/plain; charset=ISO-8859-1
> > >>
> > >> Hi everyone.
> > >> I'm sorry for the question maybe OT.
> > >> I'm trying to use R and Python to run some scripts via web interface.
> > >> I've successfully setup mod_python for Apache and the rpy module.
> > >> R needs X11 to use png() and jpeg() devices, so I have installed Xvfb
> > >> (X virtual framebuffer). I works correctly: if I set the DISPLAY
> > >> variable to point to this X server, rpy can create png files correctly
> > >> from command-line, but it doesn't work when the python script is run
> > >> from web browser.
> > >> I restarted Apache after setting the DISPLAY variable, but the
> > >> Traceback gives me always the same error, about being not able to open
> > >> the X11 device?
> > >>
> > >> Does anyone have made it work right?
> > >> How can tell Apache to run R script and forwarding X requests to my
> > >> Xvfb.
> > >>
> > >> Thanks,
> > >> Giovanni
> > >>
> > >>
> > >>
> > >> ------------------------------
> > >>
> > >> Message: 5
> > >> Date: Wed, 16 Jan 2008 11:08:28 +0100
> > >> From: "Tomislav Hengl" <hengl at science.uva.nl>
> > >> Subject: Re: [R-sig-Geo] regression kriging in gstat with skewed
> > >> distributions
> > >> To: "'G. Allegri'" <giohappy at gmail.com>
> > >> Cc: r-sig-geo at stat.math.ethz.ch
> > >> Message-ID: <001401c85827$bdac65a0$3a871291 at pcibed193>
> > >> Content-Type: text/plain; charset="windows-1250"
> > >>
> > >>
> > >> Dear Giovanni,
> > >>
> > >> Logit transformation can be automatically applied to any variables which
> > >> has a lower and upper
> > >> physical limits (e.g. 0-100%). In R, you can transform a variable to
> > >> logits by e.g.:
> > >>
> > >>
> > >>> points = read.dbf("points.dbf")
> > >>> points$SANDt = log((points$SAND/100)/(1-(points$SAND/100)))
> > >>>
> > >> After you interpolate your variable, you can back-transform the values
> > >> by using:
> > >>
> > >>
> > >>> SAND.rk = krige(fsand$call$formula, points[sel,], SPC, sand.rvgm)
> > >>>
> > >>> SAND.rk$pred=exp(SAND.rk$var1.pred)/(1+exp(SAND.rk$var1.pred))*100
> > >>>
> > >> The prediction variance can not be back-transformed, but you can use the
> > >> normalized prediction
> > >> variance by dividing it with the sampled variance. See also section
> > >> 4.2.1 of my lecture notes
> > >> (http://geostat.pedometrics.org/).
> > >>
> > >> There are many transformations that can be applied to force a normality
> > >> of your target variable (see
> > >> e.g. http://en.wikipedia.org/wiki/Data_transformation_(statistics) ).
> > >> The most generic
> > >> transformation is to work with the probability density function values
> > >> (see e.g.
> > >> http://dx.doi.org/10.1016/j.jneumeth.2006.11.004 ), this way you do not
> > >> have to think about how the
> > >> histogram looks at all. But then the interpretation of the regression
> > >> plots becomes rather
> > >> difficult.
> > >>
> > >> In any case, you should apply the transformation already to the target
> > >> variable because also a
> > >> requirement for linear regression is that the residuals are normally
> > >> distributed around the
> > >> regression line.
> > >>
> > >>
> > >> see also:
> > >> FITTING DISTRIBUTIONS WITH R (by Vito Ricci)
> > >> http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf
> > >>
> > >>
> > >> Tom Hengl
> > >> http://spatial-analyst.net
> > >>
> > >>
> > >> -----Original Message-----
> > >> From: r-sig-geo-bounces at stat.math.ethz.ch
> > >> [mailto:r-sig-geo-bounces at stat.math.ethz.ch] On Behalf Of
> > >> G. Allegri
> > >> Sent: dinsdag 15 januari 2008 15:28
> > >> To: r-sig-geo at stat.math.ethz.ch
> > >> Subject: [R-sig-Geo] regression kriging in gstat with skewed
> > >> distributions
> > >>
> > >> I'm trying to realize e regression kriging with gstat package on my
> > >> soil samples data. The response variable (ECe measuere) and covariates
> > >> appear positvely skewed.
> > >> As Tomislav Hengl suggests in its "framework for RK" [1], a logistic
> > >> transformation is proposed as a generic way to reduce the skeweness by
> > >> using the physical limits of the data.
> > >> Is it really a transformation that can be applied in the generic case
> > >> of skewed datas? I mean,in my case I have non-normal residuals (from
> > >> original data regression), and I'm trying to transform the residuals
> > >> (and not the original values) to do SK on them . Is this approach
> > >> correct?
> > >>
> > >> A related question is how to do normal score transformations (for my
> > >> residuals) in R and gstat. I know gstat doesn't manage transformations
> > >> and back-transformations, so it should be done previously in R... but
> > >> I can't find any package that permit it in a straisghtforward way.
> > >> I've found something with qqnorm(ppoints(data)) and the approx()
> > >> function. Is that all?
> > >>
> > >> Giovanni
> > >>
> > >>
> > >> [1] "A generic framework for spatial prediction of soil variables
> > >> based on regressionkriging" Geoderma 122 (1?2), 75?93.
> > >>
> > >> _______________________________________________
> > >> R-sig-Geo mailing list
> > >> R-sig-Geo at stat.math.ethz.ch
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >>
> > >>
> > >>
> > >> ------------------------------
> > >>
> > >> _______________________________________________
> > >> R-sig-Geo mailing list
> > >> R-sig-Geo at stat.math.ethz.ch
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >>
> > >>
> > >> End of R-sig-Geo Digest, Vol 53, Issue 14
> > >>
> > >> _______________________________________________
> > >> R-sig-Geo mailing list
> > >> R-sig-Geo at stat.math.ethz.ch
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >>
> > >>
> > >
> > > _______________________________________________
> > > R-sig-Geo mailing list
> > > R-sig-Geo at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >
> >
> >
> > --
> > Drs. Paul Hiemstra
> > Department of Physical Geography
> > Faculty of Geosciences
> > University of Utrecht
> > Heidelberglaan 2
> > P.O. Box 80.115
> > 3508 TC Utrecht
> > Phone: +31302535773
> > Fax: +31302531145
> > http://intamap.geo.uu.nl/~paul
> >
> >
>
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