[R] about netcdf files

[Jon Skoien]

Hi Lily,

You can ignore the first three lines, they are just for information.
Which version of raster do you have? I see that the attempt to read the 
crs-variable was not wrapped in a try-call in earlier versions. 
Upgrading might help.

Best,
Jon


On 7/27/2016 5:13 PM, lily li wrote:
> Hi Jon,
>
> I still have problems. The brick function does not work well and I 
> don't know where to check the problem. I put the error message below, 
> thanks.
>
> > pre = brick("~/Downloads/sample_precip_daily.nc 
> <http://sample_precip_daily.nc>")
> [1] "vobjtovarid4: error #F: I could not find the requsted var (or 
> dimvar) in the file!"
> [1] "var (or dimvar) name: crs"
> [1] "file name: /.../Downloads/sample_precip_daily.nc 
> <http://sample_precip_daily.nc>"
> Error in vobjtovarid4(nc, varid, allowdimvar = TRUE, verbose = verbose) :
>   Variable not found
>
>
> On Wed, Jul 27, 2016 at 1:10 AM, Jon Skoien 
> <jon.skoien at jrc.ec.europa.eu <mailto:jon.skoien at jrc.ec.europa.eu>> wrote:
>
>     I think you get the error because you passed the object from
>     nc_open(), you should rather pass the filename of the netCDF, so:
>
>     pre = brick("sample_precip_daily.nc <http://sample_precip_daily.nc>")
>     From the test-file, this gives you a RasterBrick-object with 5*9
>     pixels and 7305 layers.
>     Then you can extract data.frames of each layer with:
>     dframe = rasterToPoints(pre[[1]])
>     where 1 is the first layer, or time series with:
>     tseries = pre[3,4]
>     where 3 and 4 are the pixels in x and y-direction.
>
>     To write dframe to csv:
>     write.csv(dframe, filename = "csvfile.csv")
>     Check the function for more options.
>
>     Hope this helps you a bit further.
>     Jon
>
>
>     On 7/26/2016 9:07 PM, lily li 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
>>     <http://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
>>     <mailto: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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>>
>>         -- 
>>         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 <mailto:jon.skoien at jrc.ec.europa.eu>
>>         Tel: +39 0332 789205 <tel:%2B39%200332%20789205>
>>
>>         Disclaimer: Views expressed in this email are those of the
>>         individual and do not necessarily represent official views of
>>         the European Commission.
>>
>>
>
>     -- 
>     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 <mailto:jon.skoien at jrc.ec.europa.eu>
>     Tel:+39 0332 789205 <tel:%2B39%200332%20789205>
>
>     Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>
>

-- 
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.


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