Man pages for sapfluxnet/sapfluxnetQC1
Package with functions related to sapfluxnet project data

as_sfn_dataSfnData to sfn_data conversion
create_dicVariable dictionaries for metadata
df_accepted_to_lvl1Save the fixed datasets (metadata and data) in the LVL1...
df_copy_templatesSave the Rmd templates and the running scripts to their...
df_flag_to_lvl2_appInteractively select the data sets ready to move to level 2
df_folder_structureInitial project folder structure
df_get_data_foldersGet the folders to feed 'qc_start_process'
df_get_statusGet the status file info
df_lvl1_to_lvl2Function to pass from level 1 to level 2
df_lvl2_folder_structureBuild the folder structure of level 2
df_read_SfnDataLoad SfnData
df_received_to_acceptedMove from received to accepted data folders
df_rem_to_unitsFunction to pass from out_rem to out_units
df_report_folder_creationReports folders creation
df_reset_data_statusReset the data folder and status file for the si_code given.
df_set_statusSet the status file info
df_start_statusInitialise an empty status file
df_warn_to_remFunction to pass from out_warn to out_rem
df_whos_ready_toWho is ready the desired level?
df_write_SfnDataWrite SfnData
dl_dataLoading data from xls/xlsx ann csv files
dl_data_col_classesCheck data columns classes and set to numeric if needed
dl_dec_char_detectDecimal character detection
dl_get_si_codeGet the site code and the names of the data files (metadata,...
dl_metadataLoading metadata from xls/xlsx
dl_na_char_generatorCreate a characters vector for NA values
helloHello, World!
log_sapfluxnet_actionLogging handler action
log_sapfluxnet_formatLogs formatter
log_sapfluxnet_setupSetup handler
lvl3_processQC3 function, cleaning a little
out_appoutliers_app function
out_confirmation_appoutlier confirmation app
plot-SfnData-missing-methodplot SfnData method
qc_as_timestampConvert known bad formats to correct TIMESTAMP format and set...
qc_check_coordinatesSite coordinates checking
qc_cm_cm_hUnit conversion
qc_coordinatesCommodity function to check site coordinates
qc_coord_sign_testCoordinates sign test
qc_data_results_tableMain function to resume Data QC in one data frame
qc_download_mapsDownload maps for countries included in the database
qc_email_checkCheck if provided email directions are correct
qc_env_dicsDictionary creation for environmental_md variables
qc_env_rangesCheck ranges for environmental variables
qc_env_vars_presenceCheck for environmental variables presence
qc_ext_radiationSolar time conversion
qc_factor_valuesMetadata factor variables check
qc_fix_latlong_errorsFixing sign errors in coordinates
qc_fix_timestampFix TIMESTAMP formats
qc_get_biomeGet the biome, temperature and precipitation of a site
qc_get_biomes_spdfMake a SpatialPolygonsDataFrame object of the biomes
qc_get_sapw_mdHelper function for unit conversion
qc_get_timestepHelper function to get metadata timestep (environmental and...
qc_get_timezoneTimezones dictionary
qc_is_timestampTimeStamp format check
qc_md_colsMetadata columns check
qc_md_results_tableMain function to resume Metadata QC in one data frame
qc_mind_the_gapGaps info
qc_mind_the_gap_effGaps info
qc_out_hampel_filterHampel filter
qc_outliers_processOutliers process
qc_outliers_subsOutliers substitution
qc_out_of_rangeChecking for out of ranges values and flagging them
qc_out_removeOutliers QC
qc_plant_dicsDictionary creation for plant_md variables
qc_pl_treatmentsCheck plant treatments for misspelling and concordance errors
qc_rad_conversionRadiation units transformation
qc_range_dicRanges dictionary
qc_rhCalculation of rh from vpd and ta
qc_sapf_rangesCheck ranges for sapflow
qc_sapw_area_calculatorSapwood area calculator
qc_sapw_conversionSap flow units transformation
qc_set_timezoneSet the timezone of the TIMESTAMP
qc_site_dicsDictionary creation for site_md variables
qc_soil_textureSoil texture classification
qc_species_dicsDictionary creation for species_md variables
qc_species_namesWrapper for species names check
qc_species_names_fixVerify provided species names (spelling and correctness)
qc_species_names_infoInfo of species names spelling
qc_species_verificationCheck if sp_name and sp_ntrees coincides with plants...
qc_stand_dicsDictionary creation for stand_md variables
qc_start_processStart QC process
qc_swc_checkCheck for correct values of SWC
qc_swc_fixFix the swc values (if possible)
qc_time_intervalGetting the t_0 and t_f for trees or environmental data
qc_timestamp_concordanceCheck concordance between sapflow TIMESTAMP and env TIMESTAMP
qc_timestamp_errorsTimeStamp errors localization
qc_timestamp_nasChecking for NAs in the TIMESTAMP
qc_transf_listTransformations list
qc_transformation_varsPresence of variables needed for transformations summary
qc_units_processUnits process
qc_vpdCalculation of VPD from rh and ta
remove_dupcolsRemove columns with duplicate names
rep_sfn_renderRender the report
sfn_data2csvsfn_data2csv function
SfnData-classAn S4 class for sapfluxnet data
sfn_data_constructorCreate a SfnData object from results of Quality Checks
sfn_get_genericsSfnData custom get generics
sfn_get_methodsSfnData get methods
sfn_replacementReplacement methods
sfn_replacement_genericsReplacement generics
sfn_validityValidity method for SfnData class
show-SfnData-methodShow method for SfnData
sm_solarTIMESTAMP_addersolarTIMESTAMP adder
sm_status_updaterStatus updater to server management
sub-SfnData-numeric-ANY-missing-methodSub-setting operation
theme_sfnggplot2 theme for SAPFLUXNET plots
vis_biomePlotting a diagram of biomes
vis_environmental_responsesEnvironmental responses plot
vis_gap_linesTIMESTAMP with gaps visualization
vis_gaps_calendarGaps density visualization
vis_location_biomePlotting a diagram of biomes with sites as dots
vis_plot_the_gapPlotting an histogram for gaps intervals/gaps coverage
write_sfn_dataFunction to save the sfn_data created
sapfluxnet/sapfluxnetQC1 documentation built on March 1, 2019, 1 p.m.