convert_fluxnet_to_netcdf: ConvertSpreadsheetToNcdf.R

In aukkola/FLUXNET2015_processing: Quality Control and Data Conversion for 'FLUXNET' Data for Land Surface Modelling

ConvertSpreadsheetToNcdf.R

Description

Converts data from a FLUXNET2015 formatted spreadsheet to NetCDF.

Usage

convert_fluxnet_to_netcdf(
  site_code,
  infile,
  era_file = NA,
  out_path,
  conv_opts = get_default_conversion_options(),
  plot = c("annual", "diurnal", "timeseries"),
  site_csv_file = system.file("extdata", "Site_metadata.csv", package = "FluxnetLSM"),
  ...
)

Arguments

site_code	Fluxnet site code e.g. "AU-How"
infile	input filename, e.g. "FULLSET/FLX_AU-How_FLUXNET2015_FULLSET_HH_2001-2014_1-3.csv". La Thuile data is expected to be in the format sitecode.year.xxxx.csv, e.g. "AU-How.2001.synth.hourly.allvars.csv".
era_file	ERA-Interim input file (needed if using ERAinterim to gapfill met variables) e.g. "FULLSET/FLX_AU-How_FLUXNET2015_ERAI_HH_1989-2014_1-3.csv"
out_path	output path e.g. "./FLUXNET2016_processing/"
conv_opts	options for the conversion. See get_default_conversion_options.
plot	Should annual, diurnal and/or 14-day running mean plots be produced? Set to NA if not required.
site_csv_file	CSV file with site meta-data which is parsed to populate ancillary data provided with the flux data. By default the hard coded packaged data are used, but alternatively an external file can be provided. This limits the need to recompile the package when processing files which were not originally selected.

Details

See ?get_default_conversion_options for all conversion options.

Gapfilling options:

EraInterim: Downscaled ERAInterim estimates are provided for all meteorological variables in the FLUXNET2015 release. Any missing time steps are replaced with the corresponding ERAInterim estimates.

Statistical: Met variables gapfilled with a combination of linear interpolation (for short gaps) and copyfill (for longer gaps). Air pressure and incoming longwave radiation are synthesised from air temperature, elevation and relative humidity.

Flux variables gapfilled using a combination of linear interpolation (for short gaps) and and a linear regression against met variables (incoming shortwave, and air temperature and relative humidity, if available.). If regfill is set to NA, copyfill is used instead.

author: Anna Ukkola UNSW 2017. Main function to convert Fluxnet2015 CSV-files to NetCDF

aukkola/FLUXNET2015_processing documentation built on July 4, 2023, 12:02 p.m.