Man pages for aukkola/FLUXNET2015_processing
Quality Control and Data Conversion for 'FLUXNET' Data for Land Surface Modelling
| add_processing_info | Writes attributes common to met and flux NC files |
| add_processing_metadata | Adds processor metadata, including processor version |
| aggregate_tsteps | Aggregates original time resolution to a coarser time step |
| AnnualCycle | Plots an annual cycle |
| append_and_warn | Appends warning message and calls warning |
| append_qc | Appends information for new QC flag title |
| calc_avPrecip | Calculates mean annual precipitation |
| calc_esat | Calculates saturation vapour pressure |
| celsius_to_kelvin | Convert air temperature from Celsius to Kelvin |
| ChangeUnits | Converts units from original Fluxnet to target ALMA units |
| CheckCSVTiming | Checks that have whole number of days in dataset |
| CheckDataGaps | Checks for missing and gap-filled data and determines output... |
| CheckDataRanges | Checks that data are within specified ranges as set in the... |
| check_flx2015_version | Checks that FLUXNET2015 version defined correctly |
| check_missing | Checks which metadata are missing (correcting for OK NAs) |
| convert_fluxnet_to_netcdf | ConvertSpreadsheetToNcdf.R |
| convert_LaThuile | Converts La Thuile files to FLUXNET2015 format |
| convert_LaThuile_time | Converts La Thuile time format to Fluxnet2015 time format |
| convert_OzFlux | Converts OzFlux files to FLUXNET2015 format |
| convertToHoursMins | Utility function to convert minutes to HHMM format |
| copyfill_data | Performs copyfill gapfilling |
| Create2Uchar | Creates time stamp string |
| create_dummy_year | Function for filling missing years in La Thuile dataframe |
| CreateFluxNetcdfFile | Creates a netcdf file for flux variables |
| CreateMetNetcdfFile | Creates a netcdf file for met variables |
| create_outdir | Creates output directories and returns log output path |
| create_qc_var | Creates attributes for a new QC variable |
| CreateTimeunits | Creates time unit |
| DayNight | Finds day and night time steps |
| define_model_params | Writes model parameters as global attribute to NetCDF file |
| DiurnalCycle | Plots a diurnal cycle |
| doydate | Gets the day of month and month, given day of year |
| duplicate_columns | Duplicates columns in Fluxnet data if a variable is being... |
| FillQCvarMissing | Fills QC flags |
| findColIndices | Finds variables present in input file |
| FindExcludeEval | Finds evaluation variables to exlude |
| FindFluxInd | Finds indices for flux variables to be outputted |
| find_ind_and_qc | Find index for a variable and its QC flag |
| findStartTime | Timing_general.R |
| findTimeInfo | Extract time stamp information |
| FindTimeVarName | Finds time variable name |
| GapfillFlux | Gapfill flux variables using statistical methods |
| gapfill_LWdown_Pair | Synthesizes incoming longwave radiation and air pressure |
| GapfillMet_statistical | Gapfill meteorological variables using statistical methods |
| GapfillMet_with_ERA | Gapfills meteorological data with down-scaled ERAinterim... |
| gapfill_with_ERA | Gapfills met data |
| get_default_conversion_options | Default options for a dataset conversion |
| get_fluxdata_org_site_codes | Get all available site codes from site_status table |
| get_fluxdata_org_site_metadata | Get metadata from Fluxdata.org |
| get_fluxnet_erai_files | Gets Fluxnet ERA Interim file(s) available at a given path |
| get_fluxnet_erai_template | Gets a Fluxnet ERA interim file template (or full file name... |
| get_fluxnet_files | Gets Fluxnet file(s) available at a given path |
| get_fluxnet_file_template | Gets a Fluxnet file template (or full file name if site codes... |
| get_fluxnet_version_no | Gets Fluxnet dataset version from Fluxnet file |
| get_git_version | Gets the git version from the installed package See src/zzz.R... |
| get_lathuile_datapolicy | Gets La Thuile data policy for each site year |
| getMonthDays | Gets month indices |
| GetNumberTimesteps | Gets the number of time steps |
| get_ornl_site_codes | Get all available site codes from site_status table |
| get_ornl_site_metadata | Get metadata from ORNL |
| get_ornl_site_url_list | Get a list of ORNL site URLs from site_status table |
| get_path_site_code | Gets Fluxnet site_code from Fluxnet file. Useful when... |
| get_qc_flags | Retrieves QC flag information |
| get_site_code | Get site name from metadata |
| get_site_fluxdata_org_url | Get a single fluxdata_org site URL from site_status table |
| get_site_metadata | Get site metadata. Tries multiple methods to retrieve full... |
| get_site_metadata_from_CSV | Tries to gather metadata from the included site CSV |
| get_site_metadata_web | Tries to load metadata from known Fluxnet info sources on the... |
| get_site_ornl_url | Get a single ORNL site URL from site_status table |
| GetTimestepSize | Gets time step size |
| GetTimeUnits | Gets time units |
| GetTimingNcfile | Gets NC file timing |
| get_varnames | Gets possible varnames for FLUXNET FULLSET/SUBSET and La... |
| InitialChecks | Performs initial checks on function arguments |
| initialise_model | Finds model-specific parameters to be written to output... |
| initialise_sitelog | Initialises site log |
| is.leap | Finds leap years |
| IsWholeYrs | Checks that whole years were extracted |
| linfill_data | Performs linear interpolation gapfilling |
| log_error | Append error message to log |
| log_warning | Appends warning to site log |
| metadata_list_to_dataframe | Convert a list of metadata lists to a dataframe |
| no_error | Checks if an error has occurred |
| plot_nc | Plots standard analysis plots from netcdf data |
| preprocess_OzFlux | Pre-processes OzFlux files that have missing time steps or... |
| qc_frac | Calculates fraction of good quality data |
| ReadCSVFluxData | Reads comma-delimited text files containing Fluxnet2015 data |
| read_era | Reads ERA data and extracts time steps corresponding to obs |
| regfill_flux | Gapfills flux data using linear regression against met... |
| regpredict | Predict flux values using linear regression parameters |
| regtrain | Trains multiple linear regression for flux gap-filling... |
| Rel2SpecHumidity | Converts relative humidity to specific humidity. |
| remove_duplicates | Removes duplicate indices if a Fluxnet variable is processed... |
| retrieve_atts | Retrieve variables longnames to be written in NetCDF |
| retrieve_ranges | Retrieves acceptable variable ranges |
| retrieve_units | Retrieves original and target variable units |
| retrieve_varinfo | Retrieves variable information |
| save_metadata_list_to_csv | Write multiple site metadata to list at once |
| save_metadata_to_csv | Writes metadata to CSV, only updating non-NA data |
| site_metadata_template | Empty site metadata template, including only the site code |
| stop_and_log | Writes site log and then aborts, reporting error |
| SynthesizeLWdown | Synthesises downward longwave radiation based on Tair and rel... |
| SynthesizePSurf | Synthesises air pressure based on Tair and elevation |
| Timeseries | Plots a smoothed and non-smoothed time seris |
| update_csv_from_web | Reads all ORNL data into the CSV file |
| update_metadata | Updates old metadata with new metadata, ignoring NAs, and... |
| update_qc | Updates QC flags after gap-filling |
| VPD2RelHum | Converts VPD (hPa) to relative humidity (percentage) |
| warn_and_log | Writes site log and then aborts, reporting error |
| warn_missing_metadata | Warns about missing metadata for the site |
| write_log | Writes site log |
| Yeardays | Finds number of days per year |
