var.put.nc: Write Data to a NetCDF Variable

In RNetCDF: Interface to NetCDF Datasets

Description

Write the contents of a NetCDF variable.

Usage

var.put.nc(ncfile, variable, data, start=NA, count=NA, na.mode=0, pack=FALSE)

Arguments

ncfile	Object of class "NetCDF" which points to the NetCDF dataset (as returned from open.nc).
variable	ID or name of the NetCDF variable.
data	An R vector or array of data to be written to the NetCDF variable. Values are taken from data in the order of R vector elements, so that leftmost indices vary fastest over an array.
start	A vector of indices specifying the element where writing starts along each dimension of variable. Indices are numbered from 1 onwards, and the order of dimensions is shown by print.nc (array elements are stored sequentially with leftmost indices varying fastest). By default (start=NA), all dimensions of variable are written from the first element onwards. Otherwise, start must be a vector whose length is not less than the number of dimensions in variable (excess elements are ignored). Any NA values in vector start are set to 1.
count	A vector of integers specifying the number of values to write along each dimension of variable. The order of dimensions is the same as for start. By default (count=NA), count is set to dim(data) for an array or length(data) for a vector. Otherwise, count must be a vector whose length is not less than the number of dimensions in variable (excess elements are ignored). Any NA value in vector count indicates that the corresponding dimension should be written from the start index to the end of the dimension. Note that an unlimited dimension initially has zero length, and the dimension is extended by setting the corresponding element of count greater than the current length.
na.mode	Set the mode for handling missing values (NA) in numeric variables: 0=accept _FillValue or missing_value attribute, 1=accept only _FillValue attribute, 2=accept only missing_value attribute.
pack	Variables are packed if pack=TRUE and the attributes add_offset and scale_factor are defined. Default is FALSE.

Details

This function writes values to a NetCDF variable. Type conversion is performed by the NetCDF library, so that numeric values in R are automatically converted to the correct type of NetCDF variable.

However, text represented by R types raw and character can only be written to NetCDF type NC_CHAR. The dimensions of R raw variables map directly to NetCDF dimensions, but character variables have an implied dimension corresponding to the string length. This implied dimension must be defined explicitly as the fastest-varying dimension of the NC_CHAR variable, and it must be included as the first element of arguments start and count taken by this function.

Values of NA are supported in numeric variables if the variable's missing value attribute (as defined in na.mode) is set. They are converted to the corresponding value before writing to disk. If na.mode=0 and both attributes are defined, the value of _FillValue is used.

To reduce the storage space required by a NetCDF file, numeric variables can be "packed" into types of lower precision. The packing operation involves subtraction of attribute add_offset before division by attribute scale_factor. This packing operation is performed automatically for variables defined with the two attributes add_offset and scale_factor if argument pack is set to TRUE. If pack is FALSE, data values are assumed to be packed correctly and are written to the variable without alteration.

Data in a NetCDF variable is represented as a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The start and count arguments of this routine indicate where the writing starts and the number of values to write along each dimension.

Awkwardness arises mainly from one thing: NetCDF data are written with the last dimension varying fastest, whereas R works opposite. Thus, the order of the dimensions according to the CDL conventions (e.g., time, latitude, longitude) is reversed in the R array (e.g., longitude, latitude, time).

Note

NC_BYTE is always interpreted as signed. For best performance, it is recommended that the definition of dimensions, variables and attributes is completed before variables are read or written.

Author(s)

Pavel Michna, Milton Woods

References

http://www.unidata.ucar.edu/software/netcdf/

Examples

##  Create a new NetCDF dataset and define two dimensions
nc <- create.nc("var.put.nc")

dim.def.nc(nc, "station", 5)
dim.def.nc(nc, "time", unlim=TRUE)
dim.def.nc(nc, "max_string_length", 32)

##  Create three variables, one as coordinate variable
var.def.nc(nc, "time", "NC_INT", "time")
var.def.nc(nc, "temperature", "NC_DOUBLE", c(0,1))
var.def.nc(nc, "name", "NC_CHAR", c("max_string_length", "station"))

##  Put some missing_value attribute for temperature
att.put.nc(nc, "temperature", "missing_value", "NC_DOUBLE", -99999.9)

##  Define variable values
mytime        <- c(1:2)
mytemperature <- c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, NA, NA, 9.9)
myname        <- c("alfa", "bravo", "charlie", "delta", "echo")

dim(mytemperature) <- c(5,2)

##  Put subsets of the data:
var.put.nc(nc, "time", mytime, start=2, count=1)
var.put.nc(nc, "temperature", mytemperature[3:4,2], start=c(3,2), count=c(2,1))
var.put.nc(nc, "name", myname[3:4], start=c(NA,3), count=c(NA,2))
sync.nc(nc)

##  Put all of the data:
var.put.nc(nc, "time", mytime)
var.put.nc(nc, "temperature", mytemperature)
var.put.nc(nc, "name", myname)

close.nc(nc)

RNetCDF documentation built on May 2, 2019, 6:12 p.m.