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 |
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