Writing data to a netCDF file with R

Question

I am trying to use the data on my own .csv file to create a netCDF file using the R package "ncdf4". My dataset is composed by 3 columns: longitude, latitude and temperature and it has 2592 rows. I have been following the suggestions in the package to add the dimension and the variables to the netCDF file. Everything is fin until I want to write the temperature data on my file. I got this error:

Error in ncvar_put(nc = ncnew, varid = var_temp, data, start = c(1, 1,  : 
  ncvar_put: error: you asked to write 65160 values, but the passed data 
  array only has 2592 entries! 

What's wrong?

library(ncdf)
library(ncdf4)

TimeTable<-read.csv("time.csv",header=T,sep=",")
filename="time.nc"

xvals<-1:360
yvals<--90:90
nx<-length(xvals)
ny<-length(yvals)
lon1<-ncdim_def("longitude","degrees_east",xvals)
lat2<-ncdim_def("latitude", "degrees_north",yvals )

time<-ncdim_def("Time","months", 1:12, unlim=T )
mv <- -999 # missing value to use
var_temp<- ncvar_def("temperature", "celsius", list(lon1, lat2, time),longname="CRU_Global_1961-1990_Mean_Monthly_Surface_Temperature_Climatology",mv) 


ncnew<-nc_create(filename,list(var_temp))

print(paste("The file has",ncnew$nvars,"variables"))# 
print(paste("The file has",ncnew$ndim,"dimensions"))# 

data<-array(TimeTable$tem_1)
ncvar_put( nc=ncnew, varid=var_temp,data,start=c(1,1,1),count=c(nx,ny,1))

Could you please suggest me something? Many thanks

Answer 1

library(ncdf4)

filename="time.nc"

xvals <- seq(-177.5, 177.5, 5)
yvals <- seq(-87.5, 87.5, 5) 
nx <- length(xvals)
ny <- length(yvals)
lon1 <- ncdim_def("longitude", "degrees_east", xvals)
lat2 <- ncdim_def("latitude", "degrees_north", yvals)

time <- ncdim_def("Time","months", 1:12, unlim=TRUE)
mv <- -999 #missing value to use
var_temp <- ncvar_def("temperature", "celsius", list(lon1, lat2, time), longname="CRU_Global_1961-1990_Mean_Monthly_Surface_Temperature_Climatology", mv) 

ncnew <- nc_create(filename, list(var_temp))

print(paste("The file has", ncnew$nvars,"variables"))
#[1] "The file has 1 variables"
print(paste("The file has", ncnew$ndim,"dimensions"))
#[1] "The file has 3 dimensions"

# Some fake dataset based on latitude, to check whether the data are
# written in the correct order
data <- rep(yvals, each=nx)

# Add random -999 value to check whether missing values are correctly
# written
data[sample(1:(nx*ny), 100, replace = FALSE)] <- -999
ncvar_put(ncnew, var_temp, data, start=c(1,1,1), count=c(nx,ny,1))

# Don't forget to close the file
nc_close(ncnew)

# Verification
library(rasterVis)
out <- raster("time.nc")
levelplot(out, margin=FALSE)