Man pages for aukkola/FLUXNET2015_processing
Quality control and data conversion scripts for processing FLUXNET data for land surface modelling

add_processing_infoWrites attributes common to met and flux NC files
add_processing_metadataAdds processor metadata, including processor version
aggregate_tstepsAggregates original time resolution to a coarser time step
AnnualCyclePlots an annual cycle
append_and_warnAppends warning message and calls warning
append_qcAppends information for new QC flag
calc_avPrecipCalculates mean annual precipitation
calc_esatCalculates saturation vapour pressure
celsius_to_kelvinConvert air temperature from Celsius to Kelvin
ChangeUnitsConverts units from original Fluxnet to target ALMA units
CheckCSVTimingChecks that have whole number of days in dataset
CheckDataGapsChecks for missing and gap-filled data and determines output...
CheckDataRangesChecks that data are within specified ranges as set in the...
check_flx2015_versionChecks that FLUXNET2015 version defined correctly
check_missingChecks which metadata are missing (correcting for OK NAs)
convert_LaThuileConverts La Thuile files to FLUXNET2015 format
convert_LaThuile_timeConverts La Thuile time format to Fluxnet2015 time format
convert_OzFluxConverts OzFlux files to FLUXNET2015 format
convertToHoursMinsUtility function to convert minutes to HHMM format
copyfill_dataPerforms copyfill gapfilling
Create2UcharCreates time stamp string
create_dummy_yearFunction for filling missing years in La Thuile dataframe
CreateFluxNetcdfFileCreates a netcdf file for flux variables
CreateMetNetcdfFileCreates a netcdf file for met variables
create_outdirCreates output directories and returns log output path
create_qc_varCreates attributes for a new QC variable
CreateTimeunitsCreates time unit
DayNightFinds day and night time steps
define_model_paramsWrites model parameters as global attribute to NetCDF file
DiurnalCyclePlots a diurnal cycle
doydateGets the day of month and month, given day of year
duplicate_columnsDuplicates columns in Fluxnet data if a variable is being...
FillQCvarMissingFills QC flags with 3 (poor gap-filling) when QC flag missing...
findColIndicesFinds variables present in input file
FindExcludeEvalFinds evaluation variables to exlude
FindFluxIndFinds indices for flux variables to be outputted
find_ind_and_qcFind index for a variable and its QC flag
findTimeInfoExtract time stamp information
FindTimeVarNameFinds time variable name
GapfillFluxGapfill flux variables using statistical methods
gapfill_LWdown_PairSynthesizes incoming longwave radiation and air pressure
GapfillMet_statisticalGapfill meteorological variables using statistical methods
GapfillMet_with_ERAGapfills meteorological data with down-scaled ERAinterim...
gapfill_with_ERAGapfills met data
get_default_conversion_optionsDefault options for a dataset conversion
get_fluxdata_org_site_codesGet all available site codes from site_status table
get_fluxdata_org_site_metadataGet metadata from
get_fluxnet_erai_filesGets Fluxnet ERA Interim file(s) available at a given path
get_fluxnet_erai_templateGets a Fluxnet ERA interim file template (or full file name...
get_fluxnet_filesGets Fluxnet file(s) available at a given path
get_fluxnet_file_templateGets a Fluxnet file template (or full file name if site codes...
get_fluxnet_version_noGets Fluxnet dataset version from Fluxnet file
get_git_versionGets the git version from the installed package See src/zzz.R...
get_lathuile_datapolicyGets La Thuile data policy for each site year
getMonthDaysGets month indices
GetNumberTimestepsGets the number of time steps
get_ornl_site_codesGet all available site codes from site_status table
get_ornl_site_metadataGet metadata from ORNL
get_ornl_site_url_listGet a list of ORNL site URLs from site_status table
get_path_site_codeGets Fluxnet site_code from Fluxnet file. Useful when...
get_qc_flagsRetrieves QC flag information
get_site_codeGet site name from metadata
get_site_fluxdata_org_urlGet a single fluxdata_org site URL from site_status table
get_site_metadataGet site metadata. Tries multiple methods to retrieve full...
get_site_metadata_from_CSVTries to gather metadata from the included site CSV
get_site_metadata_webTries to load metadata from known Fluxnet info sources on the...
get_site_ornl_urlGet a single ORNL site URL from site_status table
GetTimestepSizeGets time step size
GetTimeUnitsGets time units
GetTimingNcfileGets NC file timing
get_varnamesGets possible varnames for FLUXNET FULLSET/SUBSET and La...
InitialChecksPerforms initial checks on function arguments
initialise_modelFinds model-specific parameters to be written to output...
initialise_sitelogInitialises site log
is.leapFinds leap years
IsWholeYrsChecks that whole years were extracted
linfill_dataPerforms linear interpolation gapfilling
log_errorAppend error message to log
log_warningAppends warning to site log
metadata_list_to_dataframeConvert a list of metadata lists to a dataframe
no_errorChecks if an error has occurred
plot_ncPlots standard analysis plots from netcdf data
preprocess_OzFluxPre-processes OzFlux files that have missing time steps or...
qc_fracCalculates fraction of good quality gapfilled and observed...
ReadCSVFluxDataReads comma-delimited text files containing Fluxnet2015 data
read_eraReads ERA data and extracts time steps corresponding to obs
regfill_fluxGapfills flux data using linear regression against met...
regpredictPredict flux values using linear regression parameters
regtrainTrains multiple linear regression for flux gap-filling...
Rel2SpecHumidityConverts relative humidity to specific humidity.
remove_duplicatesRemoves duplicate indices if a Fluxnet variable is processed...
retrieve_attsRetrieve variables longnames to be written in NetCDF
retrieve_rangesRetrieves acceptable variable ranges
retrieve_unitsRetrieves original and target variable units
retrieve_varinfoRetrieves variable information
save_metadata_list_to_csvWrite multiple site metadata to list at once
save_metadata_to_csvWrites metadata to CSV, only updating non-NA data
site_metadata_templateEmpty site metadata template, including only the site code
stop_and_logWrites site log and then aborts, reporting error
SynthesizeLWdownSynthesises downward longwave radiation based on Tair and rel...
SynthesizePSurfSynthesises air pressure based on Tair and elevation
TimeseriesPlots a smoothed and non-smoothed time seris
update_csv_from_webReads all ORNL data into the CSV file
update_metadataUpdates old metadata with new metadata, ignoring NAs, and...
update_qcUpdates QC flags after gap-filling
VPD2RelHumConverts VPD (hPa) to relative humidity (percentage)
warn_and_logWrites site log and then aborts, reporting error
warn_missing_metadataWarns about missing metadata for the site
write_logWrites site log
YeardaysFinds number of days per year
aukkola/FLUXNET2015_processing documentation built on Aug. 19, 2018, 3:19 p.m.