README.md

In bgctw/ncdfTools: Handling NetCDF Files

Overview

ncdfTools provides convenious functions on top of RNetCDF.

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

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

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

Installation

• install required system libraries libnetcdf-dev, udunits-bin and libudunits2-dev
• install required R packages RNetCDF package and chron package and abind package
• install.packages(c("chron","abind","RNetCDF"))
• install this package
• currently only from github

# Release stable version from CRAN
# not yet: install.packages("ncdfTools")

# The development version from GitHub using devtools:
# install.packages("devtools")
devtools::install_github("bgctw/ncdfTools")

Usage

See examples are in vignette(ncdfToolsUseCase)

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