ncdfTools-package: Set of tools to ease the handling of netCDF files

In bgctw/ncdfTools: Handling NetCDF Files

Description

Set of tools to simplify the handling of NetCDF files with the RNetCDF package. Most functions are wrappers of basic functions from the RNetCDF package to easily run combinations of these functions for frequently encountered tasks.

Details

Getting information on stored data:

• on variables: infoNcdfVars

• on dimensions: infoNcdfDims

• on attributes (global and for variables): infoNcdfAtts

• read coordinate or dimension values from ncdf file: readCoordinatesNcdf

• guess (single) variable name: readNcdfVarName

• fast reading of ncdf data: readNcdf and readNcdfDataframe

• converting data columns to unit objects: asUnitsDataFrame

Modifying NetCDF files

• copy variable values between ncdf files: modifyNcdfCopyVar

• delete variable using cdo: modifyNcdfDeleteVar

• appending history attribute: modifyNcdfAppendHistory

• copy all attributes between different variables: modifyNcdfCopyAtts

• copy attributes and dimensions between ncdf files: modifyNcdfCopyMetadata

• define several ncdf attributes at once: modifyNcdfDefAtts

• set or read the values of the time dimension in a netCDF file: modifyNcdfWriteTime and readNcdfTime

• creating a standard netCDF file: createStdNcdfFile

• creating a factor dimension: createFactorDim

• adding missing variables: modifyNcdfAddVars

• update/write a single-dimensional netCDF file by a data.frame: updateNcdfDataframe

Conversion between R and NetCDF

• convert ncdf time to POSIXct and back: POSIX2ncdf and ncdf2POSIX

Constructing and executing cdo commands producing new ncdf-Files:

• aggregate data across time: aggregateNcdf

• merge several ncdf files: transNcdfMerge

• cut outer (time) margins of Ncdf files: transNcdfCutFiles

• transpose Ncdf datacube: transNcdfRotate

• cut subset out of ncdf file: transNcdfSubset

Futher functionality:

• checking file structure compliance to CF/COARDS/MDI ncdf conventions: checkNcdfFile

• determines ncdf class from R class: classR2Ncdf

• close all open ncdf connections: closeAllNcfiles

• checking file structure compliance to CF/COARDS/MDI ncdf conventions: checkNcdfFile

• read data from FLUXNET Ncdf file: readFLUXNETNcdf

Some functionality is tailored for use at BGI department at bgc-jena.mpg.de

• read data from FLUXNET Ncdf file: readFLUXNETNcdf

Formerly in ncdf.tools but no longer supported because of dependencies:

• transform binary file to ncdf file: convertBinary2Ncdf

• convert file name to R date: .convertFilename2Date

• indexDatacube

• modifyNcdfAddDim

• registerParallel

• visualize/plot an overview of a ncdf file of 3d/4d data: plotDatacube

Author(s)

Department for Biogeochemical Integration at MPI-BGC, Jena, Germany, Jannis v. Buttlar, Thomas Wutzler

bgctw/ncdfTools documentation built on Jan. 29, 2020, 1:16 p.m.