README.md

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

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)
#> Loading required namespace: RNetCDF
#> Converted time format 'YMDH' to POSIX with column name 'DateTime'.
#> character(0)
#> Loaded BGI Fluxnet NC file: /home/twutz/R/x86_64-pc-linux-gnu-library/3.4/REddyProcNCDF/examples/Example_DE-Tha.1996.1998.hourly_selVars.nc with the following headers:
#>  *** DateTime(POSIXDate Time) year(-) month(-) day(-) hour(-) NEE(umol_m-2_s-1) Rg(W_m-2) NEE_f(umol_m-2_s-1)
head(EddyData.F)
#>              DateTime year month day hour NEE Rg NEE_f
#> 1 1996-01-01 00:30:00 1996     1   1  0.5  NA  0    NA
#> 2 1996-01-01 01:00:00 1996     1   1  1.0  NA  0    NA
#> 3 1996-01-01 01:30:00 1996     1   1  1.5  NA  0    NA
#> 4 1996-01-01 02:00:00 1996     1   1  2.0  NA  0    NA
#> 5 1996-01-01 02:30:00 1996     1   1  2.5  NA  0    NA
#> 6 1996-01-01 03:00:00 1996     1   1  3.0  NA  0    NA
# EddyData.F can now be used to initialize EddyProc R5 class 

bgctw/REddyProcNCDF documentation built on May 3, 2019, 8:59 p.m.