OPeNDAP access / OPeNDAP subsetting with R

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OPeNDAP access / OPeNDAP subsetting with R

Debasish Pai Mazumder
Hi all,

I would like to access and subset following OpeNDAP files.
server:
http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/

file name: tmax.01.2014040312.daily.grb2
<http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2>
I would like to access and subset the file. Any help will be appreciated.

with regards
-Deb

        [[alternative HTML version deleted]]

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Re: OPeNDAP access / OPeNDAP subsetting with R

Roy Mendelssohn - NOAA Federal
Look at the package ncdf4.  You can use an OPeNDAP URL in place of the file name to perform subsets.,

-Roy

> On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]> wrote:
>
> Hi all,
>
> I would like to access and subset following OpeNDAP files.
> server:
> http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
>
> file name: tmax.01.2014040312.daily.grb2
> <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2>
> I would like to access and subset the file. Any help will be appreciated.
>
> with regards
> -Deb
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: [hidden email] www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Debasish Pai Mazumder
Hi Roy,
Thanks for your response. I have tried according your suggestion but it
doesn't work.
the OPeNDAP link of the data
http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/

datafile:
tmax.01.2014040312.daily.grb2

Thanks
-Deb

On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
[hidden email]> wrote:

> Look at the package ncdf4.  You can use an OPeNDAP URL in place of the
> file name to perform subsets.,
>
> -Roy
>
> > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]>
> wrote:
> >
> > Hi all,
> >
> > I would like to access and subset following OpeNDAP files.
> > server:
> > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
> forecast_ts_9mon/2014/201404/20140403/2014040312/
> >
> > file name: tmax.01.2014040312.daily.grb2
> > <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
> forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.
> html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/
> 20140403/2014040312/tmax.01.2014040312.daily.grb2>
> > I would like to access and subset the file. Any help will be appreciated.
> >
> > with regards
> > -Deb
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] 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.
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Roy Mendelssohn - NOAA Federal
Please post the code of what you tried, as I have no idea otherwise what did or did not work for you.

-Roy

> On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <[hidden email]> wrote:
>
> Hi Roy,
> Thanks for your response. I have tried according your suggestion but it doesn't work.
> the OPeNDAP link of the data
> http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
>
> datafile:
> tmax.01.2014040312.daily.grb2
>
> Thanks
> -Deb
>
> On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <[hidden email]> wrote:
> Look at the package ncdf4.  You can use an OPeNDAP URL in place of the file name to perform subsets.,
>
> -Roy
>
> > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]> wrote:
> >
> > Hi all,
> >
> > I would like to access and subset following OpeNDAP files.
> > server:
> > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
> >
> > file name: tmax.01.2014040312.daily.grb2
> > <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2>
> > I would like to access and subset the file. Any help will be appreciated.
> >
> > with regards
> > -Deb
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] 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.
>
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
>

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: [hidden email] www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Michael Sumner-2
Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build
does work directly on grib.

Summary: download the files wholus for use on Windows, or set your own
system on Linux.

Building ncdf4 on Windows is not too hard if you know about doing that.

Cheers, Mike

On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <
[hidden email]> wrote:

> Please post the code of what you tried, as I have no idea otherwise what
> did or did not work for you.
>
> -Roy
>
> > On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <[hidden email]>
> wrote:
> >
> > Hi Roy,
> > Thanks for your response. I have tried according your suggestion but it
> doesn't work.
> > the OPeNDAP link of the data
> >
> http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
> >
> > datafile:
> > tmax.01.2014040312.daily.grb2
> >
> > Thanks
> > -Deb
> >
> > On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
> [hidden email]> wrote:
> > Look at the package ncdf4.  You can use an OPeNDAP URL in place of the
> file name to perform subsets.,
> >
> > -Roy
> >
> > > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]>
> wrote:
> > >
> > > Hi all,
> > >
> > > I would like to access and subset following OpeNDAP files.
> > > server:
> > >
> http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
> > >
> > > file name: tmax.01.2014040312.daily.grb2
> > > <
> http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2
> >
> > > I would like to access and subset the file. Any help will be
> appreciated.
> > >
> > > with regards
> > > -Deb
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > [hidden email] 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.
> >
> > **********************
> > "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> > **********************
> > Roy Mendelssohn
> > Supervisory Operations Research Analyst
> > NOAA/NMFS
> > Environmental Research Division
> > Southwest Fisheries Science Center
> > ***Note new address and phone***
> > 110 Shaffer Road
> > Santa Cruz, CA 95060
> > Phone: (831)-420-3666
> > Fax: (831) 420-3980
> > e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
> >
> > "Old age and treachery will overcome youth and skill."
> > "From those who have been given much, much will be expected"
> > "the arc of the moral universe is long, but it bends toward justice"
> -MLK Jr.
> >
> >
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
> ______________________________________________
> [hidden email] 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.
>
--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Debasish Pai Mazumder
Hi
Now I am using netcdfSubset and I am able to download the file but not sure
how to read the files. here my scripts
library("ncdf4")

gribfile<-"
http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Pacific_40km/best/dataset.html
"
download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)

gribfile<-"
http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground"

download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)


nc_open doesn't work.

which command should I use?

with regards
-Deb


On Tue, Sep 27, 2016 at 9:30 PM, Michael Sumner <[hidden email]> wrote:

> Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build
> does work directly on grib.
>
> Summary: download the files wholus for use on Windows, or set your own
> system on Linux.
>
> Building ncdf4 on Windows is not too hard if you know about doing that.
>
> Cheers, Mike
>
> On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <
> [hidden email]> wrote:
>
>> Please post the code of what you tried, as I have no idea otherwise what
>> did or did not work for you.
>>
>> -Roy
>>
>> > On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <[hidden email]>
>> wrote:
>> >
>> > Hi Roy,
>> > Thanks for your response. I have tried according your suggestion but it
>> doesn't work.
>> > the OPeNDAP link of the data
>> > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
>> forecast_ts_9mon/2014/201404/20140403/2014040312/
>> >
>> > datafile:
>> > tmax.01.2014040312.daily.grb2
>> >
>> > Thanks
>> > -Deb
>> >
>> > On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
>> [hidden email]> wrote:
>> > Look at the package ncdf4.  You can use an OPeNDAP URL in place of the
>> file name to perform subsets.,
>> >
>> > -Roy
>> >
>> > > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]>
>> wrote:
>> > >
>> > > Hi all,
>> > >
>> > > I would like to access and subset following OpeNDAP files.
>> > > server:
>> > > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
>> forecast_ts_9mon/2014/201404/20140403/2014040312/
>> > >
>> > > file name: tmax.01.2014040312.daily.grb2
>> > > <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
>> forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.
>> html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/
>> 20140403/2014040312/tmax.01.2014040312.daily.grb2>
>> > > I would like to access and subset the file. Any help will be
>> appreciated.
>> > >
>> > > with regards
>> > > -Deb
>> > >
>> > >       [[alternative HTML version deleted]]
>> > >
>> > > ______________________________________________
>> > > [hidden email] 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.
>> >
>> > **********************
>> > "The contents of this message do not reflect any position of the U.S.
>> Government or NOAA."
>> > **********************
>> > Roy Mendelssohn
>> > Supervisory Operations Research Analyst
>> > NOAA/NMFS
>> > Environmental Research Division
>> > Southwest Fisheries Science Center
>> > ***Note new address and phone***
>> > 110 Shaffer Road
>> > Santa Cruz, CA 95060
>> > Phone: (831)-420-3666
>> > Fax: (831) 420-3980
>> > e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>> >
>> > "Old age and treachery will overcome youth and skill."
>> > "From those who have been given much, much will be expected"
>> > "the arc of the moral universe is long, but it bends toward justice"
>> -MLK Jr.
>> >
>> >
>>
>> **********************
>> "The contents of this message do not reflect any position of the U.S.
>> Government or NOAA."
>> **********************
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new address and phone***
>> 110 Shaffer Road
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>>
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected"
>> "the arc of the moral universe is long, but it bends toward justice" -MLK
>> Jr.
>>
>> ______________________________________________
>> [hidden email] 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.
>>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Roy Mendelssohn - NOAA Federal
Hi Deb:

> > gribfile <- 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground'
> > download.file(gribfile,'junk.nc',mode = "wb")
> trying URL 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground'
> Content type 'application/x-netcdf' length unknown
> ....
> downloaded 4360 bytes
>
> > library(ncdf4)
> > junkFile <- nc_open('junk.nc')
> > str(junkFile)
> List of 14
>  $ filename   : chr "junk.nc"
>  $ writable   : logi FALSE
>  $ id         : int 65536
>  $ safemode   : logi FALSE
>  $ format     : chr "NC_FORMAT_CLASSIC"
>  $ is_GMT     : logi FALSE
>  $ groups     :List of 1
>   ..$ :List of 7
>   .. ..$ id   : int 65536
>   .. ..$ name : chr ""
>   .. ..$ ndims: int 4
>   .. ..$ nvars: int 7
>   .. ..$ natts: int 13
>   .. ..$ dimid: int [1:4(1d)] 0 1 2 3
>   .. ..$ fqgn : chr ""
>   .. ..- attr(*, "class")= chr "ncgroup4"
>  $ fqgn2Rindex:List of 1
>   ..$ : int 1
>  $ ndims      : num 4
>  $ natts      : num 13
>  $ dim        :List of 4
>

<snip>

I cut off the rest as that is not important for your question.

HTH,

-Roy

> On Sep 30, 2016, at 4:21 PM, Debasish Pai Mazumder <[hidden email]> wrote:
>
> Hi
> Now I am using netcdfSubset and I am able to download the file but not sure how to read the files. here my scripts
> library("ncdf4")
>
> gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Pacific_40km/best/dataset.html"
> download.file(gribfile,basename(gribfile),mode = "wb")
> x<-nc_open(gribfile)
>
> gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground"  
> download.file(gribfile,basename(gribfile),mode = "wb")
> x<-nc_open(gribfile)
>
>
> nc_open doesn't work.
>
> which command should I use?
>
> with regards
> -Deb
>
>
> On Tue, Sep 27, 2016 at 9:30 PM, Michael Sumner <[hidden email]> wrote:
> Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build does work directly on grib.
>
> Summary: download the files wholus for use on Windows, or set your own system on Linux.
>
> Building ncdf4 on Windows is not too hard if you know about doing that.
>
> Cheers, Mike
>
> On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <[hidden email]> wrote:
> Please post the code of what you tried, as I have no idea otherwise what did or did not work for you.
>
> -Roy
>
> > On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <[hidden email]> wrote:
> >
> > Hi Roy,
> > Thanks for your response. I have tried according your suggestion but it doesn't work.
> > the OPeNDAP link of the data
> > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
> >
> > datafile:
> > tmax.01.2014040312.daily.grb2
> >
> > Thanks
> > -Deb
> >
> > On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <[hidden email]> wrote:
> > Look at the package ncdf4.  You can use an OPeNDAP URL in place of the file name to perform subsets.,
> >
> > -Roy
> >
> > > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <[hidden email]> wrote:
> > >
> > > Hi all,
> > >
> > > I would like to access and subset following OpeNDAP files.
> > > server:
> > > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/
> > >
> > > file name: tmax.01.2014040312.daily.grb2
> > > <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2>
> > > I would like to access and subset the file. Any help will be appreciated.
> > >
> > > with regards
> > > -Deb
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > [hidden email] 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.
> >
> > **********************
> > "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> > **********************
> > Roy Mendelssohn
> > Supervisory Operations Research Analyst
> > NOAA/NMFS
> > Environmental Research Division
> > Southwest Fisheries Science Center
> > ***Note new address and phone***
> > 110 Shaffer Road
> > Santa Cruz, CA 95060
> > Phone: (831)-420-3666
> > Fax: (831) 420-3980
> > e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
> >
> > "Old age and treachery will overcome youth and skill."
> > "From those who have been given much, much will be expected"
> > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> >
> >
>
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
> ______________________________________________
> [hidden email] 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.
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
>

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: [hidden email] www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

______________________________________________
[hidden email] 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.
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Re: OPeNDAP access / OPeNDAP subsetting with R

Debasish Pai Mazumder
Hi Roy,
Thanks for your help. It works perfectly. if I am trying to read multiple
files similar ways, how do I do that?
with regards
-Deb



On Fri, Sep 30, 2016 at 5:53 PM, Roy Mendelssohn - NOAA Federal <
[hidden email]> wrote:

> Hi Deb:
>
> > > gribfile <- 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/
> Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.
> 641&south=44.8534&time_start=present&time_duration=PT3H&
> accept=netcdf&var=v-component_of_wind_height_above_ground,u-
> component_of_wind_height_above_ground'
> > > download.file(gribfile,'junk.nc',mode = "wb")
> > trying URL 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/
> Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.
> 641&south=44.8534&time_start=present&time_duration=PT3H&
> accept=netcdf&var=v-component_of_wind_height_above_ground,u-
> component_of_wind_height_above_ground'
> > Content type 'application/x-netcdf' length unknown
> > ....
> > downloaded 4360 bytes
> >
> > > library(ncdf4)
> > > junkFile <- nc_open('junk.nc')
> > > str(junkFile)
> > List of 14
> >  $ filename   : chr "junk.nc"
> >  $ writable   : logi FALSE
> >  $ id         : int 65536
> >  $ safemode   : logi FALSE
> >  $ format     : chr "NC_FORMAT_CLASSIC"
> >  $ is_GMT     : logi FALSE
> >  $ groups     :List of 1
> >   ..$ :List of 7
> >   .. ..$ id   : int 65536
> >   .. ..$ name : chr ""
> >   .. ..$ ndims: int 4
> >   .. ..$ nvars: int 7
> >   .. ..$ natts: int 13
> >   .. ..$ dimid: int [1:4(1d)] 0 1 2 3
> >   .. ..$ fqgn : chr ""
> >   .. ..- attr(*, "class")= chr "ncgroup4"
> >  $ fqgn2Rindex:List of 1
> >   ..$ : int 1
> >  $ ndims      : num 4
> >  $ natts      : num 13
> >  $ dim        :List of 4
> >
>
> <snip>
>
> I cut off the rest as that is not important for your question.
>
> HTH,
>
> -Roy
>
> > On Sep 30, 2016, at 4:21 PM, Debasish Pai Mazumder <[hidden email]>
> wrote:
> >
> > Hi
> > Now I am using netcdfSubset and I am able to download the file but not
> sure how to read the files. here my scripts
> > library("ncdf4")
> >
> > gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/
> NCEP/GFS/Pacific_40km/best/dataset.html"
> > download.file(gribfile,basename(gribfile),mode = "wb")
> > x<-nc_open(gribfile)
> >
> > gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/
> NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&
> east=-112.641&south=44.8534&time_start=present&time_
> duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-
> component_of_wind_height_above_ground"
> > download.file(gribfile,basename(gribfile),mode = "wb")
> > x<-nc_open(gribfile)
> >
> >
> > nc_open doesn't work.
> >
> > which command should I use?
> >
> > with regards
> > -Deb
> >
> >
> > On Tue, Sep 27, 2016 at 9:30 PM, Michael Sumner <[hidden email]>
> wrote:
> > Opendap won't work on Windows CRAN build of ncdf4, though the rgdal
> build does work directly on grib.
> >
> > Summary: download the files wholus for use on Windows, or set your own
> system on Linux.
> >
> > Building ncdf4 on Windows is not too hard if you know about doing that.
> >
> > Cheers, Mike
> >
> > On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <
> [hidden email]> wrote:
> > Please post the code of what you tried, as I have no idea otherwise what
> did or did not work for you.
> >
> > -Roy
> >
> > > On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <[hidden email]>
> wrote:
> > >
> > > Hi Roy,
> > > Thanks for your response. I have tried according your suggestion but
> it doesn't work.
> > > the OPeNDAP link of the data
> > > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
> forecast_ts_9mon/2014/201404/20140403/2014040312/
> > >
> > > datafile:
> > > tmax.01.2014040312.daily.grb2
> > >
> > > Thanks
> > > -Deb
> > >
> > > On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
> [hidden email]> wrote:
> > > Look at the package ncdf4.  You can use an OPeNDAP URL in place of the
> file name to perform subsets.,
> > >
> > > -Roy
> > >
> > > > On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <
> [hidden email]> wrote:
> > > >
> > > > Hi all,
> > > >
> > > > I would like to access and subset following OpeNDAP files.
> > > > server:
> > > > http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
> forecast_ts_9mon/2014/201404/20140403/2014040312/
> > > >
> > > > file name: tmax.01.2014040312.daily.grb2
> > > > <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
> forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.
> html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/
> 20140403/2014040312/tmax.01.2014040312.daily.grb2>
> > > > I would like to access and subset the file. Any help will be
> appreciated.
> > > >
> > > > with regards
> > > > -Deb
> > > >
> > > >       [[alternative HTML version deleted]]
> > > >
> > > > ______________________________________________
> > > > [hidden email] 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.
> > >
> > > **********************
> > > "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> > > **********************
> > > Roy Mendelssohn
> > > Supervisory Operations Research Analyst
> > > NOAA/NMFS
> > > Environmental Research Division
> > > Southwest Fisheries Science Center
> > > ***Note new address and phone***
> > > 110 Shaffer Road
> > > Santa Cruz, CA 95060
> > > Phone: (831)-420-3666
> > > Fax: (831) 420-3980
> > > e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
> > >
> > > "Old age and treachery will overcome youth and skill."
> > > "From those who have been given much, much will be expected"
> > > "the arc of the moral universe is long, but it bends toward justice"
> -MLK Jr.
> > >
> > >
> >
> > **********************
> > "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> > **********************
> > Roy Mendelssohn
> > Supervisory Operations Research Analyst
> > NOAA/NMFS
> > Environmental Research Division
> > Southwest Fisheries Science Center
> > ***Note new address and phone***
> > 110 Shaffer Road
> > Santa Cruz, CA 95060
> > Phone: (831)-420-3666
> > Fax: (831) 420-3980
> > e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
> >
> > "Old age and treachery will overcome youth and skill."
> > "From those who have been given much, much will be expected"
> > "the arc of the moral universe is long, but it bends toward justice"
> -MLK Jr.
> >
> > ______________________________________________
> > [hidden email] 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.
> > --
> > Dr. Michael Sumner
> > Software and Database Engineer
> > Australian Antarctic Division
> > 203 Channel Highway
> > Kingston Tasmania 7050 Australia
> >
> >
>
> **********************
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: [hidden email] www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.