Dear all
I'm a newbie regarding netcdf data. Today I realized that I maybe do not
understand some basics of the netcdf. I want to create a *.nc file containing
three variables for Switzerland. All data outside of the country are NAs. The
third variable is calculated from the first two variables. Basically there is
no problem to do that. I copy the file with the data of the first variable,
open this file with 'write=TRUE' (nc1 <- nc_open()), read the data to 'var1',
open the other file (nc2 <- nc_open()), read the data to variable 'var2', put
this variable to the file (nc1) and calculate the third variable based on var1
and var2.
So far everything is fine. But I figured out that when I write the data 'var2'
to nc1, all NAs in this variable are converted to the _FillValue-value.
Clearly, I expect that all NAs are converted to the _FillValue in the file, but
I do not expect that also the NAs in 'var2' (i.e. the data which can be called
in the R-console) is changed. Since I use this data for further calculations,
the NAs should remain.
Is that a bug or intended? Below you find a minimal example (adapted from the
code in the netcdf4 manual) of the – in my eye – strange behavior.
Thanks for any explanation.
Kind regards
Raphael
Minimal working example (adapted from netcdf4 manual):
library(ncdf4)
#----------------
# Make dimensions
#----------------
xvals <- 1:360
yvals <- -90:90
nx <- length(xvals)
ny <- length(yvals)
xdim <- ncdim_def('Lon','degreesE', xvals )
ydim <- ncdim_def('Lat','degreesE', yvals )
tdim <- ncdim_def('Time','days since 1900-01-01', 0, unlim=TRUE )
#---------
# Make var
#---------
mv <- 1.e30 # missing value
var_temp <- ncvar_def('Temperature','K', list(xdim,ydim,tdim), mv )
#---------------------
# Make new output file
#---------------------
output_fname <-'test_real3d.nc'
ncid_new <- nc_create( output_fname, list(var_temp))
#-------------------------------
# Put some test data in the file
#-------------------------------
data_temp <- array(0.,dim=c(nx,ny,1))
for( j in 1:ny )
for( i in 1:nx )
data_temp[i,j,1] <- sin(i/10)*sin(j/10)
# add some NAs
data_temp[1:10, 1:5, 1] <- NA
# copy data
data_temp2 <- data_temp
# show what we have
data_temp[1:12, 1:7, 1]
data_temp2[1:12, 1:7, 1]
# write to netCDF connection
ncvar_put( ncid_new, var_temp, data_temp, start=c(1,1,1), count=c(nx,ny,1))
# show what we have now
data_temp[1:12, 1:7, 1]
data_temp2[1:12, 1:7, 1]
# Why are there no more NAs in data_temp? ncvar_put changed NAs to
_FillValue-value
# But why are the NAs in data_temp2 also changed to _FillValue?
#--------------------------
# Close
#--------------------------
nc_close( ncid_new )
------------------------------------------------------------------------------------
Raphael Felber, Dr. sc.
Wissenschaftlicher Mitarbeiter, Klima und Lufthygiene
Eidgenössisches Departement für
Wirtschaft, Bildung und Forschung WBF
Agroscope
Forschungsbereich Agrarökologie und Umwelt
Reckenholzstrasse 191, 8046 Zürich
Tel. 058 468 75 11
Fax 058 468 72 01
raphael.fel...@agroscope.admin.ch<mailto:raphael.fel...@agroscope.admin.ch>
www.agroscope.ch<http://www.agroscope.ch/>
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