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List: r-sig-geo
Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
From: Edzer Pebesma <edzer.pebesma () uni-muenster ! de>
Date: 2012-05-31 13:07:20
Message-ID: 4FC76D08.6080206 () uni-muenster ! de
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You'll need to re-download the stplot.R source file, which now has a
do.repeat argument, and then run:
library(spacetime)
source("/tmp/stplot.R") # or wherever it is
library(animation)
saveGIF({
stplot(sp_time_slice, animate=0.01, col.regions=bpy.colors(),
names.attr = paste("Whatever was measured at",
format(index(sp_time_slice@time), "%H:%M")),
cex=2,cuts=seq(r[1],r[2],length.out=11), do.repeat=FALSE)
})
this also solves the title issue you mentioned.
On 05/30/2012 11:02 AM, Rawlins, Barry G. wrote:
> Yes that solves it- thanks.
>
> Re: title - yes I was thinking of a title other than the "time" and I will try \
> subtitle or putting it into an axis label - that is fine.
> Sorry, one further thing - trying to save the animation to a GIF with:
>
> library(animation)
> saveGIF(
>
> stplot(sp_time_slice, animate=1,
> col.regions=rainbow(11,start=0.0,end=0.66),cex=2,cuts=c(seq(r[1],r[2],length.out=11)))
>
> )
>
> The animated plot just goes back to the start and the GIF does not get saved - I \
> assume this is because stplot is not in a loop which is what saveGIF appears to \
> require to save an animation. Any ideas how I would resolve that? I tried:
> out<-stplot(sp_time_slice,...
>
> saveGIF
> (
> print(out)
> )
>
> But that was no good.
>
> By the way - these data are soil moisture sensor data (15 minute intervals) from a \
> hillslope responding to incident rainfall. I would be happy for you to use these as \
> example data if that is useful to you.
> Best wishes, Barry
>
> -----Original Message-----
> From: Edzer Pebesma [mailto:edzer.pebesma@uni-muenster.de]
> Sent: 30 May 2012 09:41
> To: Rawlins, Barry G.
> Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
>
> with
>
> > r= range(sp_time_slice@data$VMC) #[1] 20.7 36.8
> > stplot(sp_time_slice, animate=1,
> col.regions=rep(1,10),cex=2,cuts=c(seq(r[1],r[2],length.out=11)))
>
> I don't see points dropping, do you?
>
> On 05/30/2012 10:30 AM, Rawlins, Barry G. wrote:
> > Edzer
> >
> > Here is the data attached as an object and code to run it below:
> >
> > load(file="sp_time_slice.RData")
> >
> > range(sp_time_slice@data$VMC) #[1] 20.7 36.8
> >
> > # so with narrow ranges (20 to 37) - some symbols dropped
> >
> > stplot(sp_time_slice, animate=1, \
> > col.regions=rainbow(10,start=0.0,end=0.66),cex=2,cuts=c(seq(20,37,1.7)))
> > # with wider ranges (18, 38) all symbols plot
> >
> > stplot(sp_time_slice, animate=1, \
> > col.regions=rainbow(10,start=0.0,end=0.66),cex=2,cuts=c(seq(18,38,2)))
> > I am also struggling to get a title to plot using either
> >
> > lattice.options=list(main="Sensor Net volumetric moisture content (%)"))
> > or
> > main=list(label="Sensor Net volumetric moisture content (%)")
> >
> > Error in trellis.skeleton(formula = y2 ~ x2, cond = list(c(1L, 1L, 1L, :
> > formal argument "main" matched by multiple actual arguments
> > In addition: Warning message:
> > In seq.default(min(obj[[z]], na.rm = TRUE), max(obj[[z]], na.rm = TRUE), :
> > first element used of 'length.out' argument
> >
> > What would you use?
>
> Well, that's a nice feature request -- I haven't given it much thought,
> and main obviously is not allowed. You could use xlab="some title" or
> sub="subtitle" to see something, but I agree it's not optimal; you'd
> like to have time in subtitle when a main is given, right?
>
> >
> > Barry
> >
> > -----Original Message-----
> > From: Edzer Pebesma [mailto:edzer.pebesma@uni-muenster.de]
> > Sent: 30 May 2012 09:19
> > To: Rawlins, Barry G.
> > Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
> >
> > Barry,
> >
> > could you please provide me with a reproducible example that
> > demonstrates that min/max values passed as extremes of cuts discards
> > some points?
> >
> > I cannot reproduce it with:
> >
> > > library(sp)
> > > loadMeuse()
> > > m = meuse[1:4,]
> > > m
> > coordinates cadmium copper lead zinc elev dist om ffreq soil
> > 1 (181072, 333611) 11.7 85 299 1022 7.909 0.00135803 13.6 1 1
> > 2 (181025, 333558) 8.6 81 277 1141 6.983 0.01222430 14.0 1 1
> > 3 (181165, 333537) 6.5 68 199 640 7.800 0.10302900 13.0 1 1
> > 4 (181298, 333484) 2.6 81 116 257 7.655 0.19009400 8.0 1 2
> > lime landuse dist.m
> > 1 1 Ah 50
> > 2 1 Ah 30
> > 3 1 Ah 150
> > 4 0 Ga 270
> > > spplot(m["om"], cuts=c(8,10,12,14),col.regions=bpy.colors())
> > > spplot(m["cadmium"], cuts=c(2.6,8,11.7),col.regions=bpy.colors())
> >
> >
> > On 05/30/2012 09:57 AM, Rawlins, Barry G. wrote:
> > > Daniel and Edzer
> > >
> > > I managed to build the stplot.R function and get that working - so thanks for \
> > > that. The "cut" argument works fine and the scale does not change now as the \
> > > animation runs. For some reason I needed to make the bin range (min and max) \
> > > wider than the range of the data to make sure all the xy locations plotted in \
> > > every amimation (some were dropped otherwise) - I am not sure why that would \
> > > be the case.
> > > I will look for some instructions (presumably on other help lists) on how to \
> > > build a package from the source as that is not something I have done before, \
> > > but will be pleased to learn.
> > > Best wishes, Barry
> > >
> > >
> > > -----Original Message-----
> > > From: r-sig-geo-bounces@r-project.org [mailto:r-sig-geo-bounces@r-project.org] \
> > > On Behalf Of Daniel Nüst
> > > Sent: 29 May 2012 17:21
> > > To: r-sig-geo@r-project.org
> > > Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
> > >
> > > Am 29.05.2012 18:07, schrieb Edzer Pebesma:
> > > > On 05/29/2012 04:03 PM, Rawlins, Barry G. wrote:
> > > > > I can see a series of folders+files on the svn area - can you just give me \
> > > > > some direction on how I get the source code? Were you suggesting I just \
> > > > > take the code under R/stplot.R? And build a function from this?
> > > > I was thinking about building and installing the R package from source,
> > > > but that might be a bridge too far if you're not used to doing that.
> > > >
> > > > It might be easier to source the whole R/stplot.R file in your R session
> > > > -- that should work as well.
> > >
> > > The svn also has http access, so
> > >
> > > source("https://svn.52north.org/svn/geostatistics/main/spacetime/R/stplot.R")
> > >
> > > should do just that.
> > >
> > > /Daniel
> > >
> > > > > -----Original Message-----
> > > > > From: Edzer Pebesma [mailto:edzer.pebesma@uni-muenster.de]
> > > > > Sent: 29 May 2012 13:23
> > > > > To: Rawlins, Barry G.
> > > > > Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
> > > > >
> > > > > svn co https://svn.52north.org/svn/geostatistics/main/spacetime/
> > > > >
> > > > > will give you the updated source. Let me know if it works, otherwise
> > > > > we'll try the CRAN route (CRAN seems a bit over-worked, lately, for
> > > > > clear reasons, throwing NOTEs if you're uploading too frequent).
> > > > >
> > > > > I just noticed that the package DESCRIPTION file does not contain this
> > > > > URL -- will modify.
> > > > >
> > > > >
> > > > > On 05/29/2012 01:28 PM, Rawlins, Barry G. wrote:
> > > > > > Many thanks Edzer - it is superb to have your help on such occasions.
> > > > > >
> > > > > > Checking CRAN - the latest version of spacetime appears to be 0.7-0 - \
> > > > > > does that mean I need to wait for 0.7-1 (which you refer to) to be \
> > > > > > released?
> > > > > > I did not copy to the list because I was not sure this question was \
> > > > > > relevant to my problem.
> > > > > > Best wishes, Barry
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: r-sig-geo-bounces@r-project.org \
> > > > > > [mailto:r-sig-geo-bounces@r-project.org] On Behalf Of \
> > > > > > Edzer Pebesma
> > > > > > Sent: 29 May 2012 11:28
> > > > > > To: r-sig-geo@r-project.org
> > > > > > Subject: Re: [R-sig-Geo] Plotting with stplot, mode="xy"
> > > > > >
> > > > > > Hi Barry, the following should have worked:
> > > > > >
> > > > > > library(spacetime)
> > > > > > loadMeuse()
> > > > > > d = as.data.frame(meuse)[c("cadmium", "copper", "lead", "zinc")]
> > > > > > x = STFDF(meuse, Sys.time()+1:4, stack(d))
> > > > > > stplot(x, animate=1, col.regions=bpy.colors(),
> > > > > > cuts=c(1,10,100,1000,10000))
> > > > > >
> > > > > > but doesn't fix the legend with current spacetime on CRAN, as the 'cuts'
> > > > > > argument was not passed on to spplot.
> > > > > >
> > > > > > spacetime 0.7-1 in subversion has this fixed.
> > > > > >
> > > > > > the 'col' argument needs to be called 'col.regions'.
> > > > > >
> > > > > > On 05/28/2012 06:34 PM, Rawlins, Barry G. wrote:
> > > > > > > Hello
> > > > > > >
> > > > > > > I am trying to plot some space-time data which encompasses 3654 time
> > > > > > > intervals (15 mins each) at 84 sites.
> > > > > > >
> > > > > > > I would like to animate these data and so I have used the following \
> > > > > > > code and my STFDF object is "sp_time":
> > > > > > >
> > > > > > > colors.ten<-rainbow(10,start=0.0,end=0.66) # rainbow color scale
> > > > > > > stplot(sp_time, mode="xy", animate=1, cuts=10, at=seq(5,55,5),
> > > > > > > auto.key=T,col=colors.ten)
> > > > > > >
> > > > > > > The first plot I see is this where the points are plotted in the \
> > > > > > > correct locations:
> > > > > > >
> > > > > > > But, I wanted some bespoke rainbow colors which do not appear and I \
> > > > > > > know the z-range of the data is wider than that shown - the range is \
> > > > > > > actually between 6 and 44. When I run the animation the scale changes \
> > > > > > > each time but I would like it to be fixed so that each time slice has \
> > > > > > > the same scale. Any advice on how I can solve this? I have tried \
> > > > > > > reading the help pages on levelplot but to no avail.
> > > > > > >
> > > > > > > Thanks, Barry
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > This message (and any attachments) is for the recipient only. NERC
> > > > > > > is subject to the Freedom of Information Act 2000 and the contents
> > > > > > > of this email and any reply you make may be disclosed by NERC unless
> > > > > > > it is exempt from release under the Act. Any material supplied to
> > > > > > > NERC may be stored in an electronic records management system.
> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > R-sig-Geo mailing list
> > > > > > > R-sig-Geo@r-project.org
> > > > > > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > > > > >
> > > > >
> > > >
> > >
> > >
> >
>
--
Edzer Pebesma
Institute for Geoinformatics (ifgi), University of Münster
Weseler Straße 253, 48151 Münster, Germany. Phone: +49 251
8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de
http://www.52north.org/geostatistics e.pebesma@wwu.de
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