[R-sig-Geo] Coordinate/grid for ncdf data

[David Pierce]

If your data is weekly, then you'll want to define an unlimited time
dimension, so that your data structure looks something like this:

Radon[station_number,week_number]

And your dimensions look like something like this:

station_number[1:n_stations]
week_number[1:n_weeks] (make this unlimited with dim.def.ncdf(,unlim=TRUE)
latitude[1:n_stations]
longitude[1:n_stations]

Regards,

--Dave


Thomas Szegvary wrote:
> Dear Dave
>
> Great, that worked! Many thanks. Now I want to put more weekly data (as
> RN01
> was data for the first week of the year 2006) into the var_radon, but this
> is not possible for dim_station, as there are only 3 dimensions. Do I have
> to redefine 51 other dimensions? I tried to use list() to define the other
> dimensions, but that didn't work.
>
> Many thanks
> Thomas
>
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: David Pierce [mailto:dpierce at ucsd.edu]
> Gesendet: Donnerstag, 9. August 2007 18:25
> An: Thomas Szegvary
> Cc: 'Michael Sumner'; r-sig-geo at stat.math.ethz.ch
> Betreff: Re: AW: [R-sig-Geo] Coordinate/grid for ncdf data
>
> Hello,
>
> the reason you are getting that error from the ncdf package is because you
> have defined variable "Radon" to be a *two* dimensional array in the
> netcdf
> file.  The number of entries in dimension 1 is length(long) = 10573, and
> the
> number of entries in dimension 2 is length(lat) = 10573.
> So, the total number of entries in the array in the netcdf file is
> length(long) * length(lat) = 10573 * 10573 = 111788329.
>
> You only want to define a 2-d array when the location of data[i,j] can be
> described as (lon[i],lat[j]).  That is not the case for your data, because
> it is not on any sort of grid.  Instead, you will want to create a set of
> 3 1-dimensional arrays along the following lines:
>
> n_stations <- length(RN01)
> dim_station <- dim.def.ncdf( 'Radon_station', '-', 1:n_stations )
>
> var_lon <- var.def.ncdf( 'Longitude', 'degreesE', dim_station, 1.e30 )
> var_lat <- var.def.ncdf( 'Latitude',  'degreesN', dim_station, 1.e30 )
> var_radon <- var.def.ncdf( 'Radon',   'Bq/m2/h1', dim_stattion, 1.e30 )
>
> ncid_out <- create.ncdf( 'rn.weekly.nc', list(var_lon,var_lat,var_radon))
>
> put.var.ncdf( ncid_out, var_lon, long )
> put.var.ncdf( ncid_out, var_lat, lat  )
> put.var.ncdf( ncid_out, var_radon, RN01 )
>
> close.ncdf( ncid_out )
>
> Now, the location of data point RN01[i] is correctly described as
> (lon[i],lat[i]); compare this to what you were trying before, which was
> RN01[i,j] having the location (lon[i],lat[j]).
>
> Regards,
>
> --Dave
>
>
>
>
> Thomas Szegvary wrote:
>> I use ncdf V1.6 on Windows XP Sp2, I hava attached the sample file
>> (tab
>> delim) which contains 2 columns for coordinates long/lat and 10
>> columns for weekly averages of radon. Sp would be the best solution to
>> produce map I guess, but for time series analysis I think netcdf would
>> perform better.
>>
>> Thanks,thoams
>>
>>
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Michael Sumner [mailto:mdsumner at utas.edu.au]
>> Gesendet: Donnerstag, 9. August 2007 01:49
>> An: 'Thomas Szegvary'; r-sig-geo at stat.math.ethz.ch
>> Betreff: RE: [R-sig-Geo] Coordinate/grid for ncdf data
>>
>> Hi, can you provide an example file?
>>
>> I'd recommend avoiding NetCDF for various reasons, why don't you
>> simply add each value column from the separate files to a new column
>> in a SpatialGridDataFrame?
>>
>> That would be the recommend sp way to proceed here. If you really need
>> to create a NetCDF file, please let us know more about your OS and the
>> package/s and versions you are using (ncdf I presume?) - however such
>> questions should include the ncdf(?) package author at least.
>>
>> Cheers, Mike.
>>
>> -----Original Message-----
>> From: r-sig-geo-bounces at stat.math.ethz.ch
>> [mailto:r-sig-geo-bounces at stat.math.ethz.ch] On Behalf Of Thomas
>> Szegvary
>> Sent: Wednesday, 8 August 2007 11:13 PM
>> To: r-sig-geo at stat.math.ethz.ch
>> Subject: [R-sig-Geo] Coordinate/grid for ncdf data
>>
>> Hi!
>>
>> I have a table with 3 columns, 2 for long/lat coordinates and 1 for
>> values (radon concentration). I have data for every week of the year
>> 2006,distributed in 52 tables/files. I want to create a NetCDF file,
>> which is much easier to handle than extracting the values from 52
>> tables. I tried the following for the first dataset (i.e first week):
>>
>> #extracting coordinates and values from my tables (which have also
>> other information I don't need)
>> W01<-read.table("RN_weekly/KW01_RN.dat")
>> long<-W01$V1
>> lat<-W01$V2
>> RN01<-W01$V3
>>
>> #defining dimensions for coordinates
>> dim1 <- dim.def.ncdf( "EW","degrees", as.double(long))
>> dim2 <- dim.def.ncdf( "SN","degrees", as.double(lat))
>>
>> #defining variable for my values I want to have the time series varz
>> <- var.def.ncdf("Radon","Bq/m2/h1", list(dim1,dim2), -1,
>>           longname="Radon flux rate")
>>
>> #creating the netcdf file and filling the variable varz with the first
>> data-week from my time series nc.rn <-
>> create.ncdf("rn_weekly.nc",varz)
>> put.var.ncdf(nc.rn,varz,RN01)
>> close.ncdf(nc.rn)
>>
>>
>> The problem now is that the last step (put.var.ncdf) doesn't work,
>> because it says I am trying to "error: you asked to write 111788329
>> values, but the passed data array only has 10573* entries!". So I
>> think the problem is that I need an array with two dimensions
>> (coordinates...) for my values. But how do I get this from my tables??
>>
>>  *10573 are the pixels for my area
>>
>> Thanks for any help!
>> Thomas
>>
>>
>> __
>>
>> Thomas Szegvary
>> Institute of Environmental Geosciences Department of Geosciences
>> University of Basel Bernoullistrasse 30 CH - 4056 Basel
>>
>> Tel.  41-61-267 04 82
>> Fax. 41-61-267 04 79
>> Email: t.szegvary at unibas.ch
>> www.radon.unibas.ch
>> www.unibas.ch/environment
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>
> ---------------------------------------------------------------
> David W. Pierce        / Climate Research Division
> Scripps Inst. Oceanog. / (858) 534-8276 (voice)
> dpierce at ucsd.edu       / (858) 534-8561 (fax)
> ---------------------------------------------------------------
>
>
>


---------------------------------------------------------------
David W. Pierce        / Climate Research Division
Scripps Inst. Oceanog. / (858) 534-8276 (voice)
dpierce at ucsd.edu       / (858) 534-8561 (fax)