In bgctw/REddyProcNCDF: Reading Data from NetCDF Files for 'REddyProc'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Overview

This is an extension of the REddyProc package, which supports processing (half)hourly data from Eddy-Covariance sensors.

It adds functionality of reading half-hourly Net Ecosystem Exchange (NEE) data from NetCDF files.

Installation

NetCDF system libraries

Reading NetCDF files requires several system libraries to be installed.

Debian based OS users (Ubuntu, Docker): do from a shell:

sudo apt-get update
sudo apt-get install libnetcdf-dev
sudo apt-get install libudunits2-dev

Windows users, see ncdf home page

Mac users: TODO

R-packages

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

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

Alternatively to the RNetCDF package dependency, REddyProcNCDF also works if the ncdf4 package has been installed.

Usage

There is an example file acceseed from the REddyProc repository that stores half-hourly Net-Ecosystem-Exchange (NEE) data, that is read and displayed.

library(REddyProcNCDF)
?REddyProcNCDF

examplePath <- system.file(
  file.path('examples','Example_DE-Tha.1996.1998.hourly_selVars.nc')
  , package = "REddyProcNCDF")
EddyData.F <- fLoadFluxNCIntoDataframe(c('NEE', 'Rg', 'NEE_f'), examplePath)
head(EddyData.F)
# EddyData.F can now be used to initialize EddyProc R5 class