R help - Nov 2016 - Using map with filled.contour doesn't display map

Hi David,

Thank you for the response.  I apologize that I didn't give a more complete
example.  Here's code that recreates the issue I'm having on my system.
You'll have to enter the path to your packages and where you want to store
the downloaded file.

library("maps", lib.loc="<your library location>")
library("raster", lib.loc="<your library location>")
library("ncdf", lib.loc="<your library location>")

download.file("
http://schubert.atmos.colostate.edu/~cslocum/code/air.sig995.2012.nc",
"<your path>/temp_file.nc")
temp_file = raster("<your path>/temp_file.nc")
filledContour(temp_file, plot.axes={axis(1); axis(2); map("world2",
add=TRUE)})

When this is run, you should get a plot that shows some contours overlaid
on a map of world.  I originally wrote this several years ago. This code
worked for me with the following versions of packages: R (3.0.1); ncdf
(1.6.6); maps (2.3-6); and raster (2.1-49).

Now, on my new, upgraded system, when I run this, I get a "plot.new has not
been called yet" error.  If I then execute a plot.new() command and try the
filledContour command again, I get the contours, but no map.  As I said
below, I believe something has changed in the maps package, but I can't
find anything in the documentation on it or an indication that others are
having the same issue.  My current versions are:  R (3.3.2); ncdf4 (1.15);
maps (3.1.1); and raster (2.5-8).

I've changed from the ncdf package to the ncdf4 package, but I wouldn't
expect that to be an issue as that package is for reading netCDF files into
R and that isn't an issue (i.e. I can do a plot(temp_file) to see that the
file has been loaded properly)

Thanks for your time,
Jeff



On Fri, Nov 4, 2016 at 6:43 PM, David Winsemius <dwinsemius at
comcast.net>
wrote:
>
> > On Nov 4, 2016, at 11:26 AM, Jeff Charlton <jcharlto16 at
gmail.com> wrote:
> >
> > Hello,
> >
> > I'm trying to overlay a map on top of data showing temperatures
across
> the
> > world. The code I'm using is:
> >
> >      filledContour(tempdata, plot.axes={axis(1); axis(2);
map("world2",
> > add=TRUE)})
> >
> > where tempdata is a raster file made from a netcdf file downloaded
from
> the
> > NOAA website. The filledContour is a wrapper that translates the
raster
> > image into something that can be used by filled.contour.
> >
> > If I run the code:
> >
> >  filledContour(tempdata)
>
> It's somewhat difficult to advise since in one place you say you are
using
> filled.contour, but above you are writing filledContour (but are not saying
> where this function comes from or offering the required `library` call to
> set this up.). You are also not offering any data example. Suggest you make
> this a complete example.
>
> >
> > I get the image I want, but when I add the plot.axes parameter, I get
a
> > "plot.new has not been called yet" error in axis(1). If I
run plot.new()
> > and the original filledContour call, I get the same result as if I
just
> did
> > filledContour(tempdata) (i.e. no map is overlayed).
> >
> > The kicker in all this is that this code worked a couple of years ago.
I
> > ran into this error when I recently dusted of my code and installed
the
> > latest version of R and its various packages. I have a feeling that
> > something has changed in the maps package but I can't find any
reference
> to
> > it online.
> >
> > Can anyone help?
> >
> > Thank you,
> >
> > Jeff
> >
> > Just in case, here's my session info:
> >
> > R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit)
> > Running under: Windows 7 x64 (build 7601) Service Pack 1
> >
> > locale: [1] LC_COLLATE=English_United States.1252
LC_CTYPE=English_United
> > States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
> > LC_TIME=English_United States.1252
> >
> > attached base packages: [1] stats graphics grDevices utils datasets
> methods
> > base
> >
> > other attached packages: [1] ncdf4_1.15 maps_3.1.1 XML_3.98-1.4
> > RCurl_1.95-4.8 bitops_1.0-6 raster_2.5-8 sp_1.2-3
> >
> > loaded via a namespace (and not attached): [1] parallel_3.3.2
tools_3.3.2
> > Rcpp_0.12.7 grid_3.3.2 lattice_0.20-34
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
>
	[[alternative HTML version deleted]]

I get the error also (R3.3.1/raster2.5-8).

Works fine if I call plot.new() before calling filledContour.

Given this is a contributed package you should be corresponding with the package
maintainer if you think this solution is inappropriate or the documentation
needs fixing, but I suspect you are better off being able to initialize the plot
yourself.
-- 
Sent from my phone. Please excuse my brevity.

On November 4, 2016 9:53:18 PM PDT, Jeff Charlton <jcharlto16 at
gmail.com> wrote:
>Hi David,
>
>Thank you for the response.  I apologize that I didn't give a more
>complete
>example.  Here's code that recreates the issue I'm having on my
system.
>You'll have to enter the path to your packages and where you want to
>store
>the downloaded file.
>
>library("maps", lib.loc="<your library location>")
>library("raster", lib.loc="<your library
location>")
>library("ncdf", lib.loc="<your library location>")
>
>download.file("
>http://schubert.atmos.colostate.edu/~cslocum/code/air.sig995.2012.nc",
>"<your path>/temp_file.nc")
>temp_file = raster("<your path>/temp_file.nc")
>filledContour(temp_file, plot.axes={axis(1); axis(2);
map("world2",
>add=TRUE)})
>
>When this is run, you should get a plot that shows some contours
>overlaid
>on a map of world.  I originally wrote this several years ago. This
>code
>worked for me with the following versions of packages: R (3.0.1); ncdf
>(1.6.6); maps (2.3-6); and raster (2.1-49).
>
>Now, on my new, upgraded system, when I run this, I get a "plot.new has
>not
>been called yet" error.  If I then execute a plot.new() command and try
>the
>filledContour command again, I get the contours, but no map.  As I said
>below, I believe something has changed in the maps package, but I can't
>find anything in the documentation on it or an indication that others
>are
>having the same issue.  My current versions are:  R (3.3.2); ncdf4
>(1.15);
>maps (3.1.1); and raster (2.5-8).
>
>I've changed from the ncdf package to the ncdf4 package, but I
wouldn't
>expect that to be an issue as that package is for reading netCDF files
>into
>R and that isn't an issue (i.e. I can do a plot(temp_file) to see that
>the
>file has been loaded properly)
>
>Thanks for your time,
>Jeff
>
>
>
>On Fri, Nov 4, 2016 at 6:43 PM, David Winsemius
><dwinsemius at comcast.net>
>wrote:
>
>>
>> > On Nov 4, 2016, at 11:26 AM, Jeff Charlton <jcharlto16 at
gmail.com>
>wrote:
>> >
>> > Hello,
>> >
>> > I'm trying to overlay a map on top of data showing
temperatures
>across
>> the
>> > world. The code I'm using is:
>> >
>> >      filledContour(tempdata, plot.axes={axis(1); axis(2);
>map("world2",
>> > add=TRUE)})
>> >
>> > where tempdata is a raster file made from a netcdf file downloaded
>from
>> the
>> > NOAA website. The filledContour is a wrapper that translates the
>raster
>> > image into something that can be used by filled.contour.
>> >
>> > If I run the code:
>> >
>> >  filledContour(tempdata)
>>
>> It's somewhat difficult to advise since in one place you say you
are
>using
>> filled.contour, but above you are writing filledContour (but are not
>saying
>> where this function comes from or offering the required `library`
>call to
>> set this up.). You are also not offering any data example. Suggest
>you make
>> this a complete example.
>>
>> >
>> > I get the image I want, but when I add the plot.axes parameter, I
>get a
>> > "plot.new has not been called yet" error in axis(1). If
I run
>plot.new()
>> > and the original filledContour call, I get the same result as if I
>just
>> did
>> > filledContour(tempdata) (i.e. no map is overlayed).
>> >
>> > The kicker in all this is that this code worked a couple of years
>ago. I
>> > ran into this error when I recently dusted of my code and
installed
>the
>> > latest version of R and its various packages. I have a feeling
that
>> > something has changed in the maps package but I can't find any
>reference
>> to
>> > it online.
>> >
>> > Can anyone help?
>> >
>> > Thank you,
>> >
>> > Jeff
>> >
>> > Just in case, here's my session info:
>> >
>> > R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64
>(64-bit)
>> > Running under: Windows 7 x64 (build 7601) Service Pack 1
>> >
>> > locale: [1] LC_COLLATE=English_United States.1252
>LC_CTYPE=English_United
>> > States.1252 LC_MONETARY=English_United States.1252 [4]
LC_NUMERIC=C
>> > LC_TIME=English_United States.1252
>> >
>> > attached base packages: [1] stats graphics grDevices utils
datasets
>> methods
>> > base
>> >
>> > other attached packages: [1] ncdf4_1.15 maps_3.1.1 XML_3.98-1.4
>> > RCurl_1.95-4.8 bitops_1.0-6 raster_2.5-8 sp_1.2-3
>> >
>> > loaded via a namespace (and not attached): [1] parallel_3.3.2
>tools_3.3.2
>> > Rcpp_0.12.7 grid_3.3.2 lattice_0.20-34
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> David Winsemius
>> Alameda, CA, USA
>>
>>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

> On Nov 5, 2016, at 9:33 AM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us> wrote:
> 
> I get the error also (R3.3.1/raster2.5-8).
> 
> Works fine if I call plot.new() before calling filledContour.
It didn't "work fine" when I did that. I first briefly see a
generic plotting frame (x and y axes with no data) which was then blanked out
and replaced with a colored  "strip  map" of temperatures but no map
of continents. Further I get the message:
> library("ncdf")
Package 'ncdf' is deprecated and will be removed from CRAN shortly.
Use instead package RNetCDF or ncdf4 (for Windows from CRANextras)

I would further note that in the original sessionInfo() output there was no
instance of `ncdf` only `ncdf4`. However, that doesn't explain the problem.
The same behavior appears if I restart R and instead load ncdf4.

I was also unable to get any further plotting ... which was the original
question, I thought. In particular this failed to update the
<non-map-outlined> image.

filledContour( temp_file, plot.axes={axis(1); axis(2); map("world2",
add=TRUE); points(0,0) })

If you look at map() you see that it also messes with the par('mar')
values. I think the add=TRUE is overriding the plot=TRUE parameter to map.

I can get a subsequent `points(0,0)`-call to plot a point but the location is
not correct on the y axis.

I think you would be better advised to start with map() and then fill in the
colors using the values extracted from your NCDF file with the methods in the
setup portion of filledContour.

David.



> 
> Given this is a contributed package you should be corresponding with the
package maintainer if you think this solution is inappropriate or the
documentation needs fixing, but I suspect you are better off being able to
initialize the plot yourself.
> -- 
> Sent from my phone. Please excuse my brevity.
> 
> On November 4, 2016 9:53:18 PM PDT, Jeff Charlton <jcharlto16 at
gmail.com> wrote:
>> Hi David,
>> 
>> Thank you for the response.  I apologize that I didn't give a more
>> complete
>> example.  Here's code that recreates the issue I'm having on my
system.
>> You'll have to enter the path to your packages and where you want
to
>> store
>> the downloaded file.
>> 
>> library("maps", lib.loc="<your library
location>")
>> library("raster", lib.loc="<your library
location>")
>> library("ncdf", lib.loc="<your library
location>")
>> 
>> download.file("
>>
http://schubert.atmos.colostate.edu/~cslocum/code/air.sig995.2012.nc",
>> "<your path>/temp_file.nc")
>> temp_file = raster("<your path>/temp_file.nc")
>> filledContour(temp_file, plot.axes={axis(1); axis(2);
map("world2",
>> add=TRUE)})
>> 
>> When this is run, you should get a plot that shows some contours
>> overlaid
>> on a map of world.  I originally wrote this several years ago. This
>> code
>> worked for me with the following versions of packages: R (3.0.1); ncdf
>> (1.6.6); maps (2.3-6); and raster (2.1-49).
>> 
>> Now, on my new, upgraded system, when I run this, I get a
"plot.new has
>> not
>> been called yet" error.  If I then execute a plot.new() command
and try
>> the
>> filledContour command again, I get the contours, but no map.  As I said
>> below, I believe something has changed in the maps package, but I
can't
>> find anything in the documentation on it or an indication that others
>> are
>> having the same issue.  My current versions are:  R (3.3.2); ncdf4
>> (1.15);
>> maps (3.1.1); and raster (2.5-8).
>> 
>> I've changed from the ncdf package to the ncdf4 package, but I
wouldn't
>> expect that to be an issue as that package is for reading netCDF files
>> into
>> R and that isn't an issue (i.e. I can do a plot(temp_file) to see
that
>> the
>> file has been loaded properly)
>> 
>> Thanks for your time,
>> Jeff
>> 
>> 
>> 
>> On Fri, Nov 4, 2016 at 6:43 PM, David Winsemius
>> <dwinsemius at comcast.net>
>> wrote:
>> 
>>> 
>>>> On Nov 4, 2016, at 11:26 AM, Jeff Charlton <jcharlto16 at
gmail.com>
>> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> I'm trying to overlay a map on top of data showing
temperatures
>> across
>>> the
>>>> world. The code I'm using is:
>>>> 
>>>>     filledContour(tempdata, plot.axes={axis(1); axis(2);
>> map("world2",
>>>> add=TRUE)})
>>>> 
>>>> where tempdata is a raster file made from a netcdf file
downloaded
>> from
>>> the
>>>> NOAA website. The filledContour is a wrapper that translates
the
>> raster
>>>> image into something that can be used by filled.contour.
>>>> 
>>>> If I run the code:
>>>> 
>>>> filledContour(tempdata)
>>> 
>>> It's somewhat difficult to advise since in one place you say
you are
>> using
>>> filled.contour, but above you are writing filledContour (but are
not
>> saying
>>> where this function comes from or offering the required `library`
>> call to
>>> set this up.). You are also not offering any data example. Suggest
>> you make
>>> this a complete example.
>>> 
>>>> 
>>>> I get the image I want, but when I add the plot.axes parameter,
I
>> get a
>>>> "plot.new has not been called yet" error in axis(1).
If I run
>> plot.new()
>>>> and the original filledContour call, I get the same result as
if I
>> just
>>> did
>>>> filledContour(tempdata) (i.e. no map is overlayed).
>>>> 
>>>> The kicker in all this is that this code worked a couple of
years
>> ago. I
>>>> ran into this error when I recently dusted of my code and
installed
>> the
>>>> latest version of R and its various packages. I have a feeling
that
>>>> something has changed in the maps package but I can't find
any
>> reference
>>> to
>>>> it online.
>>>> 
>>>> Can anyone help?
>>>> 
>>>> Thank you,
>>>> 
>>>> Jeff
>>>> 
>>>> Just in case, here's my session info:
>>>> 
>>>> R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64
>> (64-bit)
>>>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>> 
>>>> locale: [1] LC_COLLATE=English_United States.1252
>> LC_CTYPE=English_United
>>>> States.1252 LC_MONETARY=English_United States.1252 [4]
LC_NUMERIC=C
>>>> LC_TIME=English_United States.1252
>>>> 
>>>> attached base packages: [1] stats graphics grDevices utils
datasets
>>> methods
>>>> base
>>>> 
>>>> other attached packages: [1] ncdf4_1.15 maps_3.1.1 XML_3.98-1.4
>>>> RCurl_1.95-4.8 bitops_1.0-6 raster_2.5-8 sp_1.2-3
>>>> 
>>>> loaded via a namespace (and not attached): [1] parallel_3.3.2
>> tools_3.3.2
>>>> Rcpp_0.12.7 grid_3.3.2 lattice_0.20-34
>>>> 
>>>>      [[alternative HTML version deleted]]
>>>> 
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/
>>> posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible
code.
>>> 
>>> David Winsemius
>>> Alameda, CA, USA
>>> 
>>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
David Winsemius
Alameda, CA, USA