[R] OPeNDAP access / OPeNDAP subsetting with R

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Sat Oct 1 01:53:56 CEST 2016 

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 <pai1981 at gmail.com> 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 <mdsumner at gmail.com> 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 <roy.mendelssohn at noaa.gov> 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 <pai1981 at gmail.com> 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 <roy.mendelssohn at noaa.gov> 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 <pai1981 at gmail.com> 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]]
> > >
> > > ______________________________________________
> > > 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.
> >
> > **********************
> > "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: Roy.Mendelssohn at noaa.gov 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: Roy.Mendelssohn at noaa.gov 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.
> 
> ______________________________________________
> 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.
> -- 
> 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: Roy.Mendelssohn at noaa.gov 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.

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