FluxnetLSM

R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile and OzFlux data releases.

URL: https://github.com/aukkola/FluxnetLSM

Maintainer: Anna Ukkola

Contributors: Anna Ukkola, Ned Haughton and Martin De Kauwe

Requires: R ≥ 3.1.0

Package is described in: Ukkola, A. M., Haughton, N., De Kauwe, M. G., Abramowitz, G., and Pitman, A. J.: FluxnetLSM R package (v1.0): a community tool for processing FLUXNET data for use in land surface modelling, Geosci. Model Dev., 10, 3379-3390, 2017

N.B. options to check for level of gap-filling have changed since v1.0

Now using separate "missing" thresholds for met and flux variables, as well as two tiers of gapfilling thresholds for met variables and a separate gap-fill check for flux variables

Installation

The package is managed with devtools.

1. Installing required packages

The FluxnetLSM package relies on three R packages: R.utils, ncdf4 and rvest. Please install these first before proceeding to install FluxnetLSM. These packages can be installed directly in R with the command install.packages(“package_name”). We also recommend installing the package devtools to aid installation.

2. Installing FluxnetLSM

To install FluxnetLSM within R software using devtools:

# install.packages("devtools")
devtools::install_github("aukkola/FluxnetLSM")

If this fails, you can download the source files by cloning the repository with the command:

$ git clone https://github.com/aukkola/FluxnetLSM.git

You can then install the package within R with the command:

install.packages("path_to_downloaded_package_files/FluxnetLSM", repos=NULL, type='source')

Usage

See examples for example usage. Three examples are provided FLUXNET2015 and La Thuile for processing a single site or multiple sites:

• single site (examples/*/example_conversion_single_site.R)

• multiple sites (examples/*/example_conversion_multiple_sites.R)

• multiple sites using parallel programming (examples/*/example_conversion_multiple_sites_parallel.R)

Troubleshooting

1. The package does not recognise the unit conversion

   Unit conversions are performed by the function ChangeUnits, you can find this under R/Conversions.R. A template is provided towards the end of this function for adding a new conversion.

2. I would like to output model-specific attributes for sites

   Model-specific attributes for each site, such as the plant functional type, can be saved in the data/Site_metadata.csv file (see example for CABLE PFT). Model-specific attributes are then set in the function initialise_model (stored in R/Model_initialisations.R) where a template for adding a new model attribute is provided. Finally, to write these in the NetCDF files, set the argument model to your model name when running the package.