Skip to contents

Apply a function over margins of a netCDF variable

Source: R/nctools-main.R
nc_apply.Rd

Reads a variable from a netCDF file, applies a function over one or more of its dimensions using [base::apply()], and writes the result to a new netCDF file.

Usage

nc_apply(
  filename,
  varid,
  MARGIN,
  FUN,
  ...,
  output = NULL,
  drop = FALSE,
  newdim = NULL,
  name = NULL,
  longname = NULL,
  units = NULL,
  compression = NA,
  verbose = FALSE,
  force_v4 = TRUE,
  ignore.case = FALSE
)

Arguments

filename

Character string giving the path to the input netCDF file.

varid

Character string giving the name of the variable to process. If missing and the file contains a single variable, that variable is used.

MARGIN

Integer or character vector specifying the dimensions to retain in the output, as in [base::apply()]. Dimension names may be used.

FUN

Function to apply.

...

Additional arguments passed to `FUN`.

output

Character string giving the path to the output netCDF file to create.

drop

Logical. Currently not implemented.

newdim

Optional numeric values for the dimension created when `FUN` returns a vector of length greater than one.

name

Optional character string giving the name of the output variable. By default, the original variable name is used.

longname

Optional character string giving the long name of the output variable. By default, a name based on `FUN` and the original variable long name is generated.

units

Optional character string giving the units of the output variable. By default, the units of the input variable are used.

compression

Optional numeric compression level for the output variable.

verbose

Logical. Currently unused.

force_v4

Logical. Currently unused internally.

ignore.case

Logical. If `TRUE`, ignore case when matching dimension names supplied in `MARGIN`.

Value

Invisibly returns `output`.

Details

The selected variable is read into memory and processed with [base::apply()]. The output retains the dimensions specified in `MARGIN`. If `FUN` returns a vector of length greater than one, an additional dimension is appended to the result; its coordinate values are taken from `newdim` when provided, or generated automatically otherwise.

See also

[nc_subset()], [write_ncdf()], [base::apply()]

Examples

if (FALSE) { # \dontrun{
## Mean over the time dimension
nc_apply(
  filename = "input.nc",
  varid = "temp",
  MARGIN = c("lon", "lat"),
  FUN = mean,
  na.rm = TRUE,
  output = "temp_mean.nc"
)

## Quantiles over the depth dimension
nc_apply(
  filename = "input.nc",
  varid = "temp",
  MARGIN = c("lon", "lat"),
  FUN = quantile,
  probs = c(0.25, 0.5, 0.75),
  newdim = c(25, 50, 75),
  output = "temp_quantiles.nc"
)
} # }