Re: [R-sig-Geo] problems with plotting STFDF
From plotKML 0.4-1 is now possible to plot results of 'krigeST'
(http://www.inside-r.org/node/176602) directly in Google Earth. This is
an example:
library(plotKML)
library(gstat)
library(sp)
library(spacetime)
sumMetricVgm - vgmST(sumMetric,
space=vgm( 4.4, Lin, 196.6, 3),
time =vgm( 2.2, Lin, 1.1, 2),
joint=vgm(34.6, Exp, 136.6, 12),
stAni=51.7)
data(air)
rr - rural[,2005-06-01/2005-06-03]
rr - as(rr,STSDF)
x1 - seq(from=6,to=15,by=1)
x2 - seq(from=48,to=55,by=1)
DE_gridded - SpatialPoints(cbind(rep(x1,length(x2)),
rep(x2,each=length(x1))),
proj4string=CRS(proj4string(rr@sp)))
gridded(DE_gridded) - TRUE
DE_pred - STF(sp=as(DE_gridded,SpatialPoints), time=rr@time)
DE_kriged - krigeST(PM10~1, data=rr, newdata=DE_pred,
modelList=sumMetricVgm)
gridded(DE_kriged@sp) - TRUE
stplot(DE_kriged)
## plot in Google Earth:
png.width = DE_kriged@sp@g...@cells.dim[1]*20
png.height = DE_kriged@sp@g...@cells.dim[2]*20
z.lim = range(DE_kriged@data, na.rm=TRUE)
plotKML(DE_kriged, png.width=png.width,
png.height=png.height, z.lim=z.lim)
## add observations points:
rr.sti - as(rr, STIDF)
plotKML(rr.sti, z.lim=z.lim)
the output looks like this:
http://plotkml.r-forge.r-project.org/DE_kriged.kmz
Note that I had to set the PNG width and height 20 time larger because
otherwise plots in Google Earth are very fuzzy.
T. Hengl
https://www.vcard.wur.nl/Views/Profile/View.aspx?id=37263
On 1-1-2014 2:55, Hodgess, Erin wrote:
Hello again! Happy New Year!
Here is the solution for this particular situation. Note: thanks to many
people for the help. Anyhow, I started with looking at page 28 in the gstat
vignette for krigeST. If you work through that, you obtain an object called
DE_kriged, which is an STFDF.
I copied some code from the following website:
(https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetime
https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetimepathrev=25)
to get the as.STIDF.STFDF lines:
# STFDF - STIDF
as.STIDF.STFDF = function(from) {
as(as(from, STSDF), STIDF)
}
setAs(STFDF, STIDF, as.STIDF.STFDF)
Now:
DE1 - as.STIDF.STFDF(DE_kriged)
DE1 is an STIDF object, which is good, but the @sp section is a Spatial Pixels
object.
Next I copied over the function kml_layer.STIDF to new_STIDF.R and added the
following section (see the note)
new.STIDF -
function (obj, dtime = , ...)
{
if (all(dtime == 0)) {
TimeSpan.begin = format(time(obj@time), %Y-%m-%dT%H:%M:%SZ)
TimeSpan.end = TimeSpan.begin
}
else {
if (length(obj@time) 1 !nzchar(dtime)) {
print(obj@time)
period - periodicity(obj@time)
dtime - period$frequency
}
TimeSpan.begin -
format(as.POSIXct(unclass(as.POSIXct(time(obj@time))) -
dtime/2, origin = 1970-01-01), %Y-%m-%dT%H:%M:%SZ)
TimeSpan.end - format(as.POSIXct(unclass(as.POSIXct(time(obj@time))) +
dtime/2, origin = 1970-01-01), %Y-%m-%dT%H:%M:%SZ)
}
if (class(obj@sp) == SpatialPoints | class(obj@sp) ==
SpatialPointsDataFrame) {
sp - SpatialPointsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPoints(obj = sp, TimeSpan.begin = TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
if (class(obj@sp) == SpatialPolygons | class(obj@sp) ==
SpatialPolygonsDataFrame) {
sp - SpatialPolygonsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPolygons(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
if (class(obj@sp) == SpatialLines | class(obj@sp) ==
SpatialLinesDataFrame) {
sp - SpatialLinesDataFrame(obj@sp, obj@data)
kml_layer.SpatialLines(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
###
# New for Spatial Pixels #
##
else {
if (class(obj@sp) == SpatialPixels | class(obj@sp) ==
SpatialPixelsDataFrame) {
sp - SpatialPixelsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPoints(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
stop(The STIDF object does not extend SpatialPoints*,
SpatialLines* or SpatialPolygons*)
}
}
}
}
}
Finally, I ran this:
library(plotKML)
plotKML version 0.4-0 (2013-11-15)
URL: http://plotkml.r-forge.r-project.org/
Warning message:
replacing previous import by ‘zoo::as.zoo’ when
Re: [R-sig-Geo] problems with plotting STFDF
Thanks, Erin; the first function should be available when loading
package spacetime; I adapted kml_layer.STIDF in plotkml (on r-forge
svn), to accomodate to your second problem.
On 01/01/2014 02:55 AM, Hodgess, Erin wrote:
Hello again! Happy New Year!
Here is the solution for this particular situation. Note: thanks to many
people for the help. Anyhow, I started with looking at page 28 in the gstat
vignette for krigeST. If you work through that, you obtain an object called
DE_kriged, which is an STFDF.
I copied some code from the following website:
(https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetime
https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetimepathrev=25)
to get the as.STIDF.STFDF lines:
# STFDF - STIDF
as.STIDF.STFDF = function(from) {
as(as(from, STSDF), STIDF)
}
setAs(STFDF, STIDF, as.STIDF.STFDF)
Now:
DE1 - as.STIDF.STFDF(DE_kriged)
DE1 is an STIDF object, which is good, but the @sp section is a Spatial
Pixels object.
Next I copied over the function kml_layer.STIDF to new_STIDF.R and added the
following section (see the note)
new.STIDF -
function (obj, dtime = , ...)
{
if (all(dtime == 0)) {
TimeSpan.begin = format(time(obj@time), %Y-%m-%dT%H:%M:%SZ)
TimeSpan.end = TimeSpan.begin
}
else {
if (length(obj@time) 1 !nzchar(dtime)) {
print(obj@time)
period - periodicity(obj@time)
dtime - period$frequency
}
TimeSpan.begin -
format(as.POSIXct(unclass(as.POSIXct(time(obj@time))) -
dtime/2, origin = 1970-01-01), %Y-%m-%dT%H:%M:%SZ)
TimeSpan.end - format(as.POSIXct(unclass(as.POSIXct(time(obj@time)))
+
dtime/2, origin = 1970-01-01), %Y-%m-%dT%H:%M:%SZ)
}
if (class(obj@sp) == SpatialPoints | class(obj@sp) ==
SpatialPointsDataFrame) {
sp - SpatialPointsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPoints(obj = sp, TimeSpan.begin = TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
if (class(obj@sp) == SpatialPolygons | class(obj@sp) ==
SpatialPolygonsDataFrame) {
sp - SpatialPolygonsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPolygons(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
if (class(obj@sp) == SpatialLines | class(obj@sp) ==
SpatialLinesDataFrame) {
sp - SpatialLinesDataFrame(obj@sp, obj@data)
kml_layer.SpatialLines(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
###
# New for Spatial Pixels #
##
else {
if (class(obj@sp) == SpatialPixels | class(obj@sp) ==
SpatialPixelsDataFrame) {
sp - SpatialPixelsDataFrame(obj@sp, obj@data)
kml_layer.SpatialPoints(obj = sp, TimeSpan.begin =
TimeSpan.begin,
TimeSpan.end = TimeSpan.end, ...)
}
else {
stop(The STIDF object does not extend SpatialPoints*,
SpatialLines* or SpatialPolygons*)
}
}
}
}
}
Finally, I ran this:
library(plotKML)
plotKML version 0.4-0 (2013-11-15)
URL: http://plotkml.r-forge.r-project.org/
Warning message:
replacing previous import by ‘zoo::as.zoo’ when loading ‘gstat’
library(gstat)
Loading required package: sp
kml_open(stuff2.kml)
KML file opened for writing...
new.STIDF(DE1,dtime=24*3600,colour=var1.pred)
Parsing to KML...
kml_close(stuff2.kml)
Closing stuff2.kml
All is well. Google Earth lets you run the kml file and show the time
change, as it should.
Hope this might help someone!
Thanks,
Erin
[[alternative HTML version deleted]]
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Heisenbergstraße 2, 48149 Münster, Germany. Phone: +49 251
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Re: [R-sig-Geo] problems with plotting STFDF
On 12/28/2013 10:02 AM, Barry Rowlingson wrote: On Sat, Dec 28, 2013 at 2:57 AM, Hodgess, Erin hodge...@uhd.edu wrote: Hello everyone! Hope you're enjoying some holiday time! I'm running into a little snag here. I'm working through the example on krigeST, which produces an STFDF object. Fine so far. However, I would like to produce a Google Earth object from that. When I use plotKML, I get: plotKML(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotKML’ for signature ‘STFDF’ Or when I use kml, I get: kml(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘kml’ for signature ‘STFDF’ What should I be doing, please? The functions are essentially saying I don't know what to do with an STFDF object. Is there any documentation that says these functions can do something sensible with STFDF data? Maybe the code is yet to be written... Barry library(plotKML) showMethods(plotKML) and also ?plotKML confirm what Barry just suggested. -- Edzer Pebesma Institute for Geoinformatics (ifgi), University of Münster Heisenbergstraße 2, 48149 Münster, Germany. Phone: +49 251 83 33081 http://ifgi.uni-muenster.de GPG key ID 0xAC227795 signature.asc Description: OpenPGP digital signature ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] problems with plotting STFDF
Hi Erin, In the spacetime package there should be a function that allows you to coerce from STFDF to STIDF class e.g. as.STIDF.STFDF (https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetime https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetimepathrev=25). Once your object is of STIDF class, then you can use kml function e.g. in a loop: x - as.STIDF.STFDF(x) kml_open(x.kml) kml_layer(x, colour=var1.pred) kml_close(x.kml) I might add plotting support for STFDF objects in the future. At the moment I do not see a special reason for this because STFDF is basically a 'compressed' / special case of STIDF, which hence needs to be 'decompressed' anyway before you can write it to KML (classes in the spacetime package are hence more creative than in the KML, but then the beauty of KML is that it is rather simple while the compression is implemented usually through zipping / KMZ). HTH T. Hengl https://www.vcard.wur.nl/Views/Profile/View.aspx?id=37263 On 29-12-2013 16:55, Edzer Pebesma wrote: On 12/28/2013 10:02 AM, Barry Rowlingson wrote: On Sat, Dec 28, 2013 at 2:57 AM, Hodgess, Erin hodge...@uhd.edu wrote: Hello everyone! Hope you're enjoying some holiday time! I'm running into a little snag here. I'm working through the example on krigeST, which produces an STFDF object. Fine so far. However, I would like to produce a Google Earth object from that. When I use plotKML, I get: plotKML(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotKML’ for signature ‘STFDF’ Or when I use kml, I get: kml(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘kml’ for signature ‘STFDF’ What should I be doing, please? The functions are essentially saying I don't know what to do with an STFDF object. Is there any documentation that says these functions can do something sensible with STFDF data? Maybe the code is yet to be written... Barry library(plotKML) showMethods(plotKML) and also ?plotKML confirm what Barry just suggested. ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] problems with plotting STFDF
I had tried x - as(x, STIDF) but it didn't like that. Thanks! Erin From: r-sig-geo-boun...@r-project.org [r-sig-geo-boun...@r-project.org] on behalf of Tomislav Hengl [he...@spatial-analyst.net] Sent: Sunday, December 29, 2013 12:12 PM To: r-sig-geo@r-project.org Subject: Re: [R-sig-Geo] problems with plotting STFDF Hi Erin, In the spacetime package there should be a function that allows you to coerce from STFDF to STIDF class e.g. as.STIDF.STFDF (https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetime https://r-forge.r-project.org/scm/viewvc.php/pkg/R/coerce.R?view=markuproot=spacetimepathrev=25). Once your object is of STIDF class, then you can use kml function e.g. in a loop: x - as.STIDF.STFDF(x) kml_open(x.kml) kml_layer(x, colour=var1.pred) kml_close(x.kml) I might add plotting support for STFDF objects in the future. At the moment I do not see a special reason for this because STFDF is basically a 'compressed' / special case of STIDF, which hence needs to be 'decompressed' anyway before you can write it to KML (classes in the spacetime package are hence more creative than in the KML, but then the beauty of KML is that it is rather simple while the compression is implemented usually through zipping / KMZ). HTH T. Hengl https://www.vcard.wur.nl/Views/Profile/View.aspx?id=37263 On 29-12-2013 16:55, Edzer Pebesma wrote: On 12/28/2013 10:02 AM, Barry Rowlingson wrote: On Sat, Dec 28, 2013 at 2:57 AM, Hodgess, Erin hodge...@uhd.edu wrote: Hello everyone! Hope you're enjoying some holiday time! I'm running into a little snag here. I'm working through the example on krigeST, which produces an STFDF object. Fine so far. However, I would like to produce a Google Earth object from that. When I use plotKML, I get: plotKML(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotKML’ for signature ‘STFDF’ Or when I use kml, I get: kml(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘kml’ for signature ‘STFDF’ What should I be doing, please? The functions are essentially saying I don't know what to do with an STFDF object. Is there any documentation that says these functions can do something sensible with STFDF data? Maybe the code is yet to be written... Barry library(plotKML) showMethods(plotKML) and also ?plotKML confirm what Barry just suggested. ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] problems with plotting STFDF
On Sat, Dec 28, 2013 at 2:57 AM, Hodgess, Erin hodge...@uhd.edu wrote: Hello everyone! Hope you're enjoying some holiday time! I'm running into a little snag here. I'm working through the example on krigeST, which produces an STFDF object. Fine so far. However, I would like to produce a Google Earth object from that. When I use plotKML, I get: plotKML(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotKML’ for signature ‘STFDF’ Or when I use kml, I get: kml(DE_kriged,var1.pred) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘kml’ for signature ‘STFDF’ What should I be doing, please? The functions are essentially saying I don't know what to do with an STFDF object. Is there any documentation that says these functions can do something sensible with STFDF data? Maybe the code is yet to be written... Barry ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
