[R-sig-Geo] put.var.ncdf error during NetCDF file creation (ncdf package)

[Steve Murray]

Dear all,


I am attempting to convert 10 NetCDF files into a single NetCDF file, due to the data input requirements of a model I hope to use. I am using the ncdf package, version 1.6. The data are global-scale water values, on a monthly basis for 10 years (ie. 120 months of data in total; at present the data are separated by year, with 12 months of data in each file - mrunoff_1986 through to mrunoff_1995). For each month there are 720 longitude x 360 latitude values, each with a corresponding runoff value (although some of these may be NAs).


Here is my code so far:



# READ IN NetCDF FILES FROM DISK


library(ncdf)


year <- 1986:1995

file_list <- paste("mrunoff-",year,".nc", sep="")

file_list


start <- 1986


for (i in file_list) {

        assign(paste("netcdf_",start,"_temp", sep=""),open.ncdf(i))

        start = start+1

          }


# Start converting 10 files into 1


latitude <- get.var.ncdf(netcdf_1986_temp, "Lat")

longitude <- get.var.ncdf(netcdf_1986_temp, "Lon")

month <- get.var.ncdf(netcdf_1986_temp, "Mon")


year <- 1986:1995


mrunoff_1986 <- get.var.ncdf(netcdf_1986_temp, "mrunoff")

mrunoff_1987 <- get.var.ncdf(netcdf_1987_temp, "mrunoff")

mrunoff_1988 <- get.var.ncdf(netcdf_1988_temp, "mrunoff")

mrunoff_1989 <- get.var.ncdf(netcdf_1989_temp, "mrunoff")

mrunoff_1990 <- get.var.ncdf(netcdf_1990_temp, "mrunoff")

mrunoff_1991 <- get.var.ncdf(netcdf_1991_temp, "mrunoff")

mrunoff_1992 <- get.var.ncdf(netcdf_1992_temp, "mrunoff")

mrunoff_1993 <- get.var.ncdf(netcdf_1993_temp, "mrunoff")

mrunoff_1994 <- get.var.ncdf(netcdf_1994_temp, "mrunoff")

mrunoff_1995 <- get.var.ncdf(netcdf_1995_temp, "mrunoff")



# Define variable dimensions


dimx <- dim.def.ncdf("Lon", "deg E", as.double(longitude))

dimy <- dim.def.ncdf("Lat", "deg N", as.double(latitude))

month <- dim.def.ncdf("Mon", "Months: Jan 86=1, Dec 95=120)", 1:120)

year <- dim.def.ncdf("Year", "year", year)


# Assign data: extract mrunoff from each of the 10 files and put into one place


mrunoff_data <- dim.def.ncdf("mrunoff",
"mm/month", c(mrunoff_1986, mrunoff_1987, mrunoff_1988, mrunoff_1989,
mrunoff_1990, mrunoff_1991, mrunoff_1992, mrunoff_1993, mrunoff_1994,
mrunoff_1995))


# Define runoff variable


mrunoff_dims <- var.def.ncdf("mrunoff_out", "mm/month", list(dimx, dimy, month), -9999.0, "Global Monthly Runoff for 1986-1995", "double")


# Create file


mrunoff_file <- create.ncdf("mrunoff.nc", mrunoff_dims)


# Put mrunoff data into the file


put.var.ncdf(mrunoff_file, mrunoff_dims, mrunoff_data)


# Write to disk


# close.ncdf(mrunoff_file)





However, when I run the code, I get the following error message:


> put.var.ncdf(mrunoff_file, mrunoff_dims, mrunoff_data)

Error in put.var.ncdf(mrunoff_file, mrunoff_dims, mrunoff_data) : 

  put.var.ncdf: error: you asked to write 31104000 values, but the passed data array only has 8 entries!



I can understand where the 31104000 comes from ((720*360)*12)*10, but am confused as to why only 8 values are being passed to put.var.ncdf. I therefore tried doing a couple of tests to shed some light on this:


> length(dimx); length(dimy); length(mrunoff_dims); length(mrunoff_data)

[1] 8

[1] 8

[1] 9

[1] 8



> str(dimx); str(dimy)

List of 8

 $ name         : chr "Lon"

 $ units        : chr "deg E"

 $ vals         : num [1:720] 0.25 0.75 1.25 1.75 2.25 2.75 3.25 3.75 4.25 4.75 ...

 $ len          : int 720

 $ id           : num -1

 $ unlim        : logi FALSE

 $ dimvarid     : num -1

 $ create_dimvar: logi TRUE

 - attr(*, "class")= chr "dim.ncdf"


List of 8

 $ name         : chr "Lat"

 $ units        : chr "deg N"

 $ vals         : num [1:360] -89.8 -89.2 -88.8 -88.2 -87.8 ...

 $ len          : int 360

 $ id           : num -1

 $ unlim        : logi FALSE

 $ dimvarid     : num -1

 $ create_dimvar: logi TRUE

 - attr(*, "class")= chr "dim.ncdf"



> str(mrunoff_dims); str(mrunoff_data)

List of 9

 $ name    : chr "mrunoff_out"

 $ units   : chr "mm/month"

 $ missval : num -9999

 $ longname: chr "Global Monthly Runoff for 1986-1995"

 $ id      : num -1

 $ prec    : chr "double"

 $ dim     :List of 3

  ..$ :List of 8

  .. ..$ name         : chr "Lon"

  .. ..$ units        : chr "deg E"

  .. ..$ vals         : num [1:720] 0.25 0.75 1.25 1.75 2.25 2.75 3.25 3.75 4.25 4.75 ...

  .. ..$ len          : int 720

  .. ..$ id           : num -1

  .. ..$ unlim        : logi FALSE

  .. ..$ dimvarid     : num -1

  .. ..$ create_dimvar: logi TRUE

  .. ..- attr(*, "class")= chr "dim.ncdf"

  ..$ :List of 8

  .. ..$ name         : chr "Lat"

  .. ..$ units        : chr "deg N"

  .. ..$ vals         : num [1:360] -89.8 -89.2 -88.8 -88.2 -87.8 ...

  .. ..$ len          : int 360

  .. ..$ id           : num -1

  .. ..$ unlim        : logi FALSE

  .. ..$ dimvarid     : num -1

  .. ..$ create_dimvar: logi TRUE

  .. ..- attr(*, "class")= chr "dim.ncdf"

  ..$ :List of 8

  .. ..$ name         : chr "Mon"

  .. ..$ units        : chr "Months since Jan 1986 (Jan 86 =1)"

  .. ..$ vals         : int [1:120] 1 2 3 4 5 6 7 8 9 10 ...

  .. ..$ len          : int 120

  .. ..$ id           : num -1

  .. ..$ unlim        : logi FALSE

  .. ..$ dimvarid     : num -1

  .. ..$ create_dimvar: logi TRUE

  .. ..- attr(*, "class")= chr "dim.ncdf"

 $ ndims   : int 3

 $ unlim   : logi FALSE

 - attr(*, "class")= chr "var.ncdf"


List of 8

 $ name         : chr "mrunoff"

 $ units        : chr "mm/month"

 $ vals         : num [1:31104000] NA NA NA NA NA NA NA NA NA NA ...

 $ len          : int 31104000

 $ id           : num -1

 $ unlim        : logi FALSE

 $ dimvarid     : num -1

 $ create_dimvar: logi TRUE

 - attr(*, "class")= chr "dim.ncdf"




As you can see from this, the length of the objects and the $len values of the objects differ - the latter being the intended values - plus all the data (e.g. 1:31104000) appear to be present in the str of the object. I'm struggling to see therefore why only 8 'bits' of data are being passed on.


Any help would be much appreciated.


Thanks for any suggestions,


Steve


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