Error when trying to import NetCDF to R

Question

I\' struggeling to open a NetCDF file in R. When I try to open it with

library(ncdf)
# read in NetCDF file
maize.nc<-open.ncdf(\"C:/Users/Jo/Desktop/pft_         


        

Answer 1

The dump from ncdump -k gives the netcdf file format as netCDF-4. I was able to open the file with the ncdf4 package since ncdf does not seem to be backwards compatible with version 4 files:

"However, the ncdf package does not provide an interface for netcdf version 4 files."

from the ncdf4 documentation.

library(ncdf4)
mycdf <- nc_open(file.choose(), verbose = TRUE, write = FALSE)
timedata <- ncvar_get(mycdf,'time')
lat <- ncvar_get(mycdf,'latitude')
long <- ncvar_get(mycdf,'longitude')
harvestdata <- ncvar_get(mycdf,'harvest')

str(harvestdata)

gives

num [1:79, 1:78, 1:32, 1:199] NA NA NA NA NA NA NA NA NA NA ...

Answer 2

I think that the harvest maize netcdf file is simply corrupt, or not even a netcdf file (file name does not say anything about the real contents). Try and open it in NCView or dump using ncdump, if those tool also fails your file is corrupt or incomplete. In addition, if you want us to help, you need to make your file available.