[R] about netcdf files
lily li
chocold12 at gmail.com
Tue Jul 26 23:00:07 CEST 2016
Here are the results. Yes, I tried to read netcdf files, but cannot grasp
the contents. Thanks for helping out.
> str(pre1)
List of 14
$ filename : chr "~/Downloads/sample_precip_daily.nc"
$ writable : logi FALSE
$ id : int 262144
$ safemode : logi FALSE
$ format : chr "NC_FORMAT_CLASSIC"
$ is_GMT : logi FALSE
$ groups :List of 1
..$ :List of 7
.. ..$ id : int 262144
.. ..$ name : chr ""
.. ..$ ndims: int 3
.. ..$ nvars: int 4
.. ..$ natts: int 48
.. ..$ dimid: int [1:3(1d)] 0 1 2
.. ..$ fqgn : chr ""
.. ..- attr(*, "class")= chr "ncgroup4"
$ fqgn2Rindex:List of 1
..$ : int 1
$ ndims : num 3
$ natts : num 48
$ dim :List of 3
..$ time:List of 11
.. ..$ name : chr "time"
.. ..$ len : int 7305
.. ..$ unlim : logi FALSE
.. ..$ group_index : int 1
.. ..$ group_id : int 262144
.. ..$ id : int 0
.. ..$ dimvarid :List of 5
.. .. ..$ id : int 1
.. .. ..$ group_index: int 1
.. .. ..$ group_id : int 262144
.. .. ..$ list_index : num -1
.. .. ..$ isdimvar : logi TRUE
.. .. ..- attr(*, "class")= chr "ncid4"
.. ..$ units : chr "days since 1900-01-01 00:00:00"
.. ..$ calendar : chr "gregorian"
.. ..$ vals : num [1:7305(1d)] 38716 38717 38718 38719 38720 ...
.. ..$ create_dimvar: logi TRUE
.. ..- attr(*, "class")= chr "ncdim4"
..$ lat :List of 10
.. ..$ name : chr "lat"
.. ..$ len : int 5
.. ..$ unlim : logi FALSE
.. ..$ group_index : int 1
.. ..$ group_id : int 262144
.. ..$ id : int 1
.. ..$ dimvarid :List of 5
.. .. ..$ id : int 2
.. .. ..$ group_index: int 1
.. .. ..$ group_id : int 262144
.. .. ..$ list_index : num -1
.. .. ..$ isdimvar : logi TRUE
.. .. ..- attr(*, "class")= chr "ncid4"
.. ..$ units : chr "degrees_north"
.. ..$ vals : num [1:5(1d)] 39.8 39.9 40 40 40.1
.. ..$ create_dimvar: logi TRUE
.. ..- attr(*, "class")= chr "ncdim4"
..$ lon :List of 10
.. ..$ name : chr "lon"
.. ..$ len : int 9
.. ..$ unlim : logi FALSE
.. ..$ group_index : int 1
.. ..$ group_id : int 262144
.. ..$ id : int 2
.. ..$ dimvarid :List of 5
.. .. ..$ id : int 3
.. .. ..$ group_index: int 1
.. .. ..$ group_id : int 262144
.. .. ..$ list_index : num -1
.. .. ..$ isdimvar : logi TRUE
.. .. ..- attr(*, "class")= chr "ncid4"
.. ..$ units : chr "degrees_east"
.. ..$ vals : num [1:9(1d)] 254 254 254 254 255 ...
.. ..$ create_dimvar: logi TRUE
.. ..- attr(*, "class")= chr "ncdim4"
$ unlimdimid : num -1
$ nvars : num 1
$ var :List of 1
..$ precipitation:List of 22
.. ..$ id :List of 5
.. .. ..$ id : num 0
.. .. ..$ group_index: num -1
.. .. ..$ group_id : int 262144
.. .. ..$ list_index : num 1
.. .. ..$ isdimvar : logi FALSE
.. .. ..- attr(*, "class")= chr "ncid4"
.. ..$ name : chr "precipitation"
.. ..$ ndims : int 3
.. ..$ natts : int 9
.. ..$ size : int [1:3] 9 5 7305
.. ..$ dimids : int [1:3] 2 1 0
.. ..$ prec : chr "float"
.. ..$ units : chr "mm"
.. ..$ longname : chr "Precipitation"
.. ..$ group_index : int 1
.. ..$ chunksizes : logi NA
.. ..$ storage : num 1
.. ..$ shuffle : logi FALSE
.. ..$ compression : logi NA
.. ..$ dims : list()
.. ..$ dim :List of 3
.. .. ..$ :List of 10
.. .. .. ..$ name : chr "lon"
.. .. .. ..$ len : int 9
.. .. .. ..$ unlim : logi FALSE
.. .. .. ..$ group_index : int 1
.. .. .. ..$ group_id : int 262144
.. .. .. ..$ id : int 2
.. .. .. ..$ dimvarid :List of 5
.. .. .. .. ..$ id : int 3
.. .. .. .. ..$ group_index: int 1
.. .. .. .. ..$ group_id : int 262144
.. .. .. .. ..$ list_index : num -1
.. .. .. .. ..$ isdimvar : logi TRUE
.. .. .. .. ..- attr(*, "class")= chr "ncid4"
.. .. .. ..$ units : chr "degrees_east"
.. .. .. ..$ vals : num [1:9(1d)] 254 254 254 254 255 ...
.. .. .. ..$ create_dimvar: logi TRUE
.. .. .. ..- attr(*, "class")= chr "ncdim4"
.. .. ..$ :List of 10
.. .. .. ..$ name : chr "lat"
.. .. .. ..$ len : int 5
.. .. .. ..$ unlim : logi FALSE
.. .. .. ..$ group_index : int 1
.. .. .. ..$ group_id : int 262144
.. .. .. ..$ id : int 1
.. .. .. ..$ dimvarid :List of 5
.. .. .. .. ..$ id : int 2
.. .. .. .. ..$ group_index: int 1
.. .. .. .. ..$ group_id : int 262144
.. .. .. .. ..$ list_index : num -1
.. .. .. .. ..$ isdimvar : logi TRUE
.. .. .. .. ..- attr(*, "class")= chr "ncid4"
.. .. .. ..$ units : chr "degrees_north"
.. .. .. ..$ vals : num [1:5(1d)] 39.8 39.9 40 40 40.1
.. .. .. ..$ create_dimvar: logi TRUE
.. .. .. ..- attr(*, "class")= chr "ncdim4"
.. .. ..$ :List of 11
.. .. .. ..$ name : chr "time"
.. .. .. ..$ len : int 7305
.. .. .. ..$ unlim : logi FALSE
.. .. .. ..$ group_index : int 1
.. .. .. ..$ group_id : int 262144
.. .. .. ..$ id : int 0
.. .. .. ..$ dimvarid :List of 5
.. .. .. .. ..$ id : int 1
.. .. .. .. ..$ group_index: int 1
.. .. .. .. ..$ group_id : int 262144
.. .. .. .. ..$ list_index : num -1
.. .. .. .. ..$ isdimvar : logi TRUE
.. .. .. .. ..- attr(*, "class")= chr "ncid4"
.. .. .. ..$ units : chr "days since 1900-01-01 00:00:00"
.. .. .. ..$ calendar : chr "gregorian"
.. .. .. ..$ vals : num [1:7305(1d)] 38716 38717 38718 38719
38720 ...
.. .. .. ..$ create_dimvar: logi TRUE
.. .. .. ..- attr(*, "class")= chr "ncdim4"
.. ..$ varsize : int [1:3] 9 5 7305
.. ..$ unlim : logi FALSE
.. ..$ make_missing_value: logi TRUE
.. ..$ missval : num -9999
.. ..$ hasAddOffset : logi FALSE
.. ..$ hasScaleFact : logi FALSE
.. ..- attr(*, "class")= chr "ncvar4"
- attr(*, "class")= chr "ncdf4"
On Tue, Jul 26, 2016 at 2:52 PM, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
> Hi Lily:
>
> I doubt the mail-list would pass through the netcdf file. Instead, could
> you do the following, and post the results:
>
> library(ncdf4
> pre1 = nc_open('sample_precip_daily.nc')
> str(pre1)
> nc_close(pre1)
>
> I have a feeling you haven't worked much with netcdf files. I will try to
> find a tutorial also to help you along.
>
> Thanks,
>
> -Roy
>
> > On Jul 26, 2016, at 12:07 PM, lily li <chocold12 at gmail.com> wrote:
> >
> > Thanks for your reply. But it says "Error in (function (classes, fdef,
> > mtable)):
> > unable to find an inherited method for function 'brick' for signature
> > 'ncdf4' "
> >
> > The dataset is attached. It contains daily precipitation data for 20
> years,
> > within a rectangle, so that there are several grid points. I use the code
> > to open it, but don't know how to get csv files, while each file contains
> > continuous daily precipitation data for each grid cell.
> > pre1 = nc_open('sample_precip_daily.nc')
> > pre1
> > pre1_rd = ncvar_get(pre1, 'precipitation')
> > nc_close(pre1)
> >
> > Thanks for your help.
> >
> > On Tue, Jul 26, 2016 at 4:08 AM, Jon Skoien <jon.skoien at jrc.ec.europa.eu
> >
> > wrote:
> >
> >> You could try with the brick function from the raster package.
> >>
> >> bvar = brick(netcdfName)
> >>
> >> This uses the ncdf4 functions for opening and reading the netcdf, but
> >> makes it easier to extract data for each day:
> >>
> >> p1 = rasterToPoints(bvar[[1]])
> >> and write p1 to csv.
> >>
> >> Best,
> >> Jon
> >>
> >>
> >>
> >> On 7/26/2016 6:54 AM, lily li wrote:
> >>
> >>> Hi all,
> >>>
> >>> I have a problem in opening netcdf files. If one netcdf file contains
> >>> longitude, latitude, and daily precipitation. How to relate each
> >>> precipitation record to its associated location, and export them as csv
> >>> files? Thanks.
> >>>
> >>> I just use nc_open(), ncvar_get(), but it is not very helpful. Thanks
> for
> >>> any ideas.
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
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> >>> 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.
> >>>
> >>>
> >> --
> >> Jon Olav Skøien
> >> Joint Research Centre - European Commission
> >> Institute for Space, Security & Migration
> >> Disaster Risk Management Unit
> >>
> >> Via E. Fermi 2749, TP 122, I-21027 Ispra (VA), ITALY
> >>
> >> jon.skoien at jrc.ec.europa.eu
> >> Tel: +39 0332 789205
> >>
> >> Disclaimer: Views expressed in this email are those of the individual
> and
> >> do not necessarily represent official views of the European Commission.
> >>
> > ______________________________________________
> > 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.
>
>
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