thr3ads.net - R help - [R] about netcdf files [Aug 2016]

If this information is useful, please help other people find it:
Share via:

lily li

2016-Jul-26 19:07 UTC

[R] about netcdf files

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]]
>>
>> ______________________________________________
>> 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.
>>
>>
> --
> Jon Olav Sk?ien
> 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.
>

Roy Mendelssohn - NOAA Federal

2016-Jul-26 20:52 UTC

head link

[R] about netcdf files

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]]
>>> 
>>> ______________________________________________
>>> 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.
>>> 
>>> 
>> --
>> Jon Olav Sk?ien
>> 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.

lily li

2016-Jul-26 21:00 UTC

head link

[R] about netcdf files

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]]
> >>>
> >>> ______________________________________________
> >>> 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.
> >>>
> >>>
> >> --
> >> Jon Olav Sk?ien
> >> 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.
>
>
	[[alternative HTML version deleted]]

lily li

2016-Jul-26 21:04 UTC

head link

[R] about netcdf files

How to read continuous daily precipitation at each grid cell, and then
export to a csv file? Later, there should be several csv files, each
represents daily precipitation data for one grid cell. Thanks a lot.

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]]
> >>>
> >>> ______________________________________________
> >>> 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.
> >>>
> >>>
> >> --
> >> Jon Olav Sk?ien
> >> 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.
>
>
	[[alternative HTML version deleted]]

Jon Skoien

2016-Jul-27 07:10 UTC

head link

[R] about netcdf files

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")
 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]]
>
>         ______________________________________________
>         R-help at r-project.org <mailto: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.
>
>
>     -- 
>     Jon Olav Sk?ien
>     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 Sk?ien
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.


	[[alternative HTML version deleted]]

Jon Skoien

2016-Jul-27 15:31 UTC

head link

[R] about netcdf files

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]]
>>
>>             ______________________________________________
>>             R-help at r-project.org <mailto: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.
>>
>>
>>         -- 
>>         Jon Olav Sk?ien
>>         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 Sk?ien
>     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 Sk?ien
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.


	[[alternative HTML version deleted]]

lily li

2016-Jul-27 16:46 UTC

head link

[R] about netcdf files

Hi Jon,

The versions are: raster_2.5-2 sp_1.2-3


On Wed, Jul 27, 2016 at 9:31 AM, Jon Skoien <jon.skoien at
jrc.ec.europa.eu>
wrote:
> 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")
> [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"
> 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>
> 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")
>> 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')
>> 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>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]]
>>>>
>>>> ______________________________________________
>>>> 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>
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible
code.
>>>>
>>>>
>>> --
>>> Jon Olav Sk?ien
>>> 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 <%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 Sk?ien
>> 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.
>>
>>
>
> --
> Jon Olav Sk?ien
> 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.
>
>
	[[alternative HTML version deleted]]

lily li

2016-Aug-01 17:35 UTC

head link

[R] about netcdf files

Hi all,

I can read the data, but how to plot it using ggplot or something? In this
case, x-axis should be longitude, and y-axis should be latitude. I tried to
plot using raster function, but the x and y axes are from 0 to 1.
Thanks again.

The code is like this:
pre1 = nc_open('sample_precip_daily.nc')
pre.3d = ncvar_get(pre1, 'precipitation')

require(raster)
rplot = t(pre.3d[, , 1])
r = raster(rplot[nrow(rplot):1, ]
plot(r)


On Tue, Jul 26, 2016 at 1:07 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]]
>>>
>>> ______________________________________________
>>> 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.
>>>
>>>
>> --
>> Jon Olav Sk?ien
>> 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.
>>
>
>
	[[alternative HTML version deleted]]

Roy Mendelssohn - NOAA Federal

2016-Aug-01 17:46 UTC

head link

[R] about netcdf files

Hi Lily:

If you download the vignette to my xtractomatic package 
(http://coastwatch.pfeg.noaa.gov/xtracto/index.html) there are any number of
examples using ggplot2 to make maps from netcdf data,

HTH,

-Roy
> On Aug 1, 2016, at 10:35 AM, lily li <chocold12 at gmail.com> wrote:
> 
> Hi all,
> 
> I can read the data, but how to plot it using ggplot or something? In this
> case, x-axis should be longitude, and y-axis should be latitude. I tried to
> plot using raster function, but the x and y axes are from 0 to 1.
> Thanks again.
> 
> The code is like this:
> pre1 = nc_open('sample_precip_daily.nc')
> pre.3d = ncvar_get(pre1, 'precipitation')
> 
> require(raster)
> rplot = t(pre.3d[, , 1])
> r = raster(rplot[nrow(rplot):1, ]
> plot(r)
> 
> 
> On Tue, Jul 26, 2016 at 1:07 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]]
>>>> 
>>>> ______________________________________________
>>>> 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.
>>>> 
>>>> 
>>> --
>>> Jon Olav Sk?ien
>>> 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.
>>> 
>> 
>> 
> 
> 	[[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.

R help - Aug 2016 - about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files

[R] about netcdf files