Hi,
Well, I did it, but all my script was on the first message. I don't have any
other variables. I am just reading a NCDF file and trying to read the
variable "tasmax", that has values of temperatures.
The only "new" information I have is the header of the NCDF file
(Spain02D_tasmax.nc), that I have obtained by running "ncdump" command.
netcdf Spain02D_tasmax {
dimensions:
time = 21275 ;
lat = 40 ;
lon = 68 ;
variables:
double time(time) ;
time:long_name = "Time variable" ;
time:units = "days since 1950-01-01 00:00:00" ;
double lat(lat) ;
lat:standard_name = "latitude" ;
lat:long_name = "latitude" ;
lat:units = "degrees north" ;
double lon(lon) ;
lon:standard_name = "longitude" ;
lon:long_name = "longitude" ;
lon:units = "degrees east" ;
double tasmax(time, lat, lon) ;
tasmax:long_name = "Daily maximum temperature" ;
tasmax:units = "degrees Celsius" ;
tasmax:missing_value = "-9999.0f" ;
// global attributes:
:Info = "Data generated for the esTcena project (
http://www.meteo.unican.es/projects/esTcena)" ;
:Institution = "IFCA-UC" ;
:Conventions = "CF-1.0" ;
:conventionsURL = "
http://www.cgd.ucar.edu/cms/eaton/cf-metadata/index.html"; ;
:creation_date = "20-Sep-2010 09:34:26" ;
data:
(...)
tasmax =
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, 14.0840393066406, 14.4718475341797, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN,
(...)
As we can see, "tasmax" has a lot of NaN (not a number) values. And the
missing_value of the file is "-9999.0f".
As we can see in following lines, the error occurs just when the function
"get.var.ncdf" is trying to set the missing values to NA.
> library(ncdf)
> file<-open.ncdf("Spain02D_tasmax.nc")
> temp<-get.var.ncdf(file,"tasmax",verbose=TRUE)
[1] "get.var.ncdf: entering. Here is varid:"
[1] "tasmax"
[1] "checking to see if passed varid is actually a dimvar"
[1] "entering vobjtodimname with varid= tasmax"
[1] "vobjtodimname: is a character type varid. This file has 3 dims"
[1] "vobjtodimname: no cases found, returning FALSE"
[1] "get.var.ncdf: isdimvar: FALSE"
[1] "vobjtovarid: entering with varid=tasmax"
[1] "Variable named tasmax found in file with varid= 4"
[1] "vobjtovarid: returning with varid deduced from name; varid= 4"
[1] "get.var.ncdf: ending up using varid= 4"
[1] "ndims: 3"
[1] "get.var.ncdf: varsize:"
[1] 68 40 21275
[1] "get.var.ncdf: start:"
[1] 1 1 1
[1] "get.var.ncdf: count:"
[1] 68 40 21275
[1] "get.var.ncdf: totvarsize: 57868000"
[1] "Getting var of type 4 (1=short, 2=int, 3=float, 4=double, 5=char,
6=byte)"
[1] "get.var.ncdf: C call returned 0"
[1] "count.nodegen: 68 Length of data: 57868000"
[2] "count.nodegen: 40 Length of data: 57868000"
[3] "count.nodegen: 21275 Length of data: 57868000"
[1] "get.var.ncdf: final dims of returned array:"
[1] 68 40 21275
[1] "varid: 4"
[1] "nc$varid2Rindex: 0" "nc$varid2Rindex: 0" "nc$varid2Rindex: 0"
[4] "nc$varid2Rindex: 1"
[1] "nc$varid2Rindex[varid]: 1"
[1] "get.var.ncdf: setting missing values to NA"
Error en mv * 1e-05 : non-numeric argument to binary operator
I think that the error is related to this procedure: to set missing values
to NA. But I am not sure, as I told you I am a newbie and I did not see any
error like this before (even in discussion lists in the web).
If any of you that have worked with NCDF files in R could help me, even if
you know any other packages or commands to read this values, I would be
really really grateful.
Thank you very much for your attention! Sorry about my poor English.
Charles
On Wed, Oct 27, 2010 at 3:46 PM, jim holtman <jholt...@gmail.com> wrote:
> put:
>
> options(error=utils::recover)
>
> in your script so that when an error occurs you are dropped into the
> 'browser' so that you can examine the variables at that point in time.
> There are several references on how to use the debugging tools in R
> that will help you resolve your problem. We can not tell from the
> information you provided what the problem is. You need to at least
> provide provide commented, minimal, self-contained, reproducible code
> so other can reproduce the error and provide feed back.
>
> On Wed, Oct 27, 2010 at 9:27 AM, Charles Novaes de Santana
> <charles.sant...@imedea.uib-csic.es> wrote:
> > Hi everyone,
> >
> > I am a newbie in R and in this discussion list. I am trying to use R
> package
> > "ncdf" to read values of temperature from a NCDF file. I did it before to
> > another file using the function "get.var.ncdf", but now there is an error
> > that I can not solve, and I would really appreciate if you could help me.
> >
> > I am using R version 2.11.1 (2010-05-31) in a machine with Linux
> > 2.6.26-2-amd64.
> >
> >> library(ncdf)
> >> file_temp<-open.ncdf("File.nc")
> >> temp<-get.var.ncdf(file_temp,"tasmax",verbose=TRUE)
> > [1] "get.var.ncdf: entering. Here is varid:"
> > [1] "tasmax"
> > [1] "checking to see if passed varid is actually a dimvar"
> > [1] "entering vobjtodimname with varid= tasmax"
> > [1] "vobjtodimname: is a character type varid. This file has 3 dims"
> > [1] "vobjtodimname: no cases found, returning FALSE"
> > [1] "get.var.ncdf: isdimvar: FALSE"
> > [1] "vobjtovarid: entering with varid=tasmax"
> > [1] "Variable named tasmax found in file with varid= 4"
> > [1] "vobjtovarid: returning with varid deduced from name; varid= 4"
> > [1] "get.var.ncdf: ending up using varid= 4"
> > [1] "ndims: 3"
> > [1] "get.var.ncdf: varsize:"
> > [1] 68 40 21275
> > [1] "get.var.ncdf: start:"
> > [1] 1 1 1
> > [1] "get.var.ncdf: count:"
> > [1] 68 40 21275
> > [1] "get.var.ncdf: totvarsize: 57868000"
> > [1] "Getting var of type 4 (1=short, 2=int, 3=float, 4=double, 5=char,
> > 6=byte)"
> > [1] "get.var.ncdf: C call returned 0"
> > [1] "count.nodegen: 68 Length of data: 57868000"
> > [2] "count.nodegen: 40 Length of data: 57868000"
> > [3] "count.nodegen: 21275 Length of data: 57868000"
> > [1] "get.var.ncdf: final dims of returned array:"
> > [1] 68 40 21275
> > [1] "varid: 4"
> > [1] "nc$varid2Rindex: 0" "nc$varid2Rindex: 0" "nc$varid2Rindex: 0"
> > [4] "nc$varid2Rindex: 1"
> > [1] "nc$varid2Rindex[varid]: 1"
> > [1] "get.var.ncdf: setting missing values to NA"
> > Error en mv * 1e-05 : non-numeric argument to binary operator
> >
> > Thank you very much for your attention!
> >
> > Cheers,
> >
> > Charles
> >
> > --
> > Um axé! :)
> >
> > --
> > Charles Novaes de Santana
> > PhD student - Global Change
> > Laboratorio Internacional de Cambio Global
> > Department of Global Change Research
> > Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
> > Calle Miquel Marques 21, 07006
> > Esporles - Islas Baleares - España
> >
> > [[alternative HTML version deleted]]
> >
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > 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.
> >
> >
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
--
Um axé! :)
--
Charles Novaes de Santana
PhD student - Global Change
Laboratorio Internacional de Cambio Global
Department of Global Change Research
Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
Calle Miquel Marques 21, 07006
Esporles - Islas Baleares - España
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