Package index • REddyProc

All functions
`BerkeleyJulianDateToPOSIXct()`	BerkeleyJulianDateToPOSIXct
`DEGebExample`	Eddy covariance data from Gebesee crop site, Germany
`Example_DETha98`	Eddy covariance data from Tharandt, Germany
`LRC_NonRect_computeGPPGradient()`	Gradient of `LRC_NonRect_predictGPP()`
`LRC_NonRect_computeLRCGradient()`	Gradient of `LRC_NonRect_predictLRC()`
`LRC_NonRect_getOptimizedParamPos()`	Get the positions of the parameters to optimize for given Fixed
`LRC_NonRect_getParamNames()`	`LRC_NonRect_getParamNames`: return the parameter names used by this Light Response Curve Function
`LRC_NonRect_predictGPP()`	Nonrectangular Light Response function for GPP
`LRC_NonRect_predictLRC()`	Nonrectangular Hyperbolic Light Response function: (Gilmanov et al., 2003)
`LRC_computeCost()`	Computing residual sum of squares for predictions vs. data of NEE
`LRC_computeLRCGradient()`	Gradient of the Light Response Function
`LRC_fitLRC()`	Optimize rectangular hyperbolic light response curve in one window
`LRC_getOptimizedParamPos()`	Get the positions of the parameters to optimize for given Fixed
`LRC_getParamNames()`	LRC_getParamNames
`LRC_getPriorLocation()`	LRC_getPriorLocation
`LRC_getPriorScale()`	LRC_getPriorScale
`LRC_isParameterInBounds()`	isParameterInBounds
`LRC_optimLRC()`	optim LRC
`LRC_optimLRCBounds()`	Optimize parameters with refitting with some fixed parameters if outside bounds
`LRC_optimLRCOnAdjustedPrior()`	optimLRCOnAdjustedPrior
`LRC_predictGPP()`	Light Response function for GPP
`LRC_predictLRC()`	Light Response Function
`LightResponseCurveFitter-class` `LightResponseCurveFitter`	R5 reference parent class for describing the NEP ~ PAR relationship
`LogisticSigmoidLRCFitter-class`	Class `"LogisticSigmoidLRCFitter"`
`LogisticSigmoidLRCFitter()`	LogisticSigmoidLRCFitter
`LogisticSigmoidLRCFitter_predictGPP()`	LogisticSigmoidLRCFitter predictGPP
`NonrectangularLRCFitter-class`	Class `"NonrectangularLRCFitter"`
`NonrectangularLRCFitter()`	NonrectangularLRCFitter
`NonrectangularLRCFitter_getParameterNames()`	NonrectangularLRCFitter getParameterNames
`NonrectangularLRCFitter_predictGPP()`	NonrectangularLRCFitter predictGPP
`POSIXctToBerkeleyJulianDate()`	POSIXctToBerkeleyJulianDate
`REddyProc-package` `REddyProc`	Post Processing of (Half-)Hourly Eddy-Covariance Measurements
`REddyProc_defaultunits()`	Get the default units for given variables
`RHLightResponseCostC()`	RHLightResponseCostC
`RectangularLRCFitter-class` `RectangularLRCFitter`	R5 reference class for the Rectangular Light response curve
`RectangularLRCFitter()`	RectangularLRCFitter
`RectangularLRCFitterCVersion-class` `RectangularLRCFitterCVersion`	R5 reference class C-version for the Rectangular Light response curve
`RectangularLRCFitterCVersion()`	RectangularLRCFitterCVersion
`RectangularLRCFitterCVersion_computeCost()`	Computing residual sum of squares for predictions vs. data of NEE
`RectangularLRCFitter_computeGPPGradient()`	RectangularLRCFitter_computeGPPGradient
`RectangularLRCFitter_predictGPP()`	RectangularLRCFitter predictGPP
`applyWindows()`	apply a function to several windows of a data.frame
`.computeRecoNight()`	recompute ecosystem respiration at nighttime with nighttime reference
`.partGPAssociateSpecialRows()`	associate each row with the previous and next row from a subset of rows
`estimate_vpd_from_dew()`	Estimate VPD from assuming dewpoint at daily minimum temperature
`extract_FN15()`	extract processing results with columns corresponding to Fluxnet15 release
`fCalcAVPfromVMFandPress()`	fCalcAVPfromVMFandPress
`fCalcETfromLE()`	fCalcETfromLE
`fCalcExtRadiation()`	fCalcExtRadiation
`fCalcPotRadiation()`	fCalcPotRadiation
`fCalcRHfromAVPandTair()`	fCalcRHfromAVPandTair
`fCalcSVPfromTair()`	fCalcSVPfromTair
`fCalcVPDfromRHandTair()`	fCalcVPDfromRHandTair
`fCheckHHTimeSeries()`	fCheckHHTimeSeries
`fConvertCtoK()`	fConvertCtoK
`fConvertGlobalToVisible()`	fConvertGlobalToVisible
`fConvertKtoC()`	fConvertKtoC
`fConvertTimeToPosix()`	fConvertTimeToPosix
`fConvertVisibleWm2toPhotons()`	fConvertVisibleWm2toPhotons
`fKeepColumnAttributes()`	fKeepColumnAttributes
`fLloydTaylor()`	Temperature dependence of soil respiration
`fLoadAmeriflux22()`	Read basic variables from Ameriflux standard (as of 2022) files
`fLoadEuroFlux16()`	fLoadEuroFlux16
`fLoadFluxnet15()`	Read a file in the format of Fluxnet 2015 release
`fLoadTXTIntoDataframe()`	Load text file with one header and one unit row into data frame
`fSplitDateTime()`	fSplitDateTime
`fWriteDataframeToFile()`	fWriteDataframeToFile
`fWriteFrench23()`	fWriteFrench23
`fillNAForward()`	replace NA by value of previous record
`filterLongRuns()`	filterLongRuns
`filterLongRunsInVector()`	filterLongRunsInVector
`filter_entire_days()`	filter entire days
`filter_years_eop()`	filter years eop
`getAmerifluxToBGC05VariableNameMapping()`	getAmerifluxToBGC05VariableNameMapping
`getBGC05ToAmerifluxVariableNameMapping()`	getBGC05ToAmerifluxVariableNameMapping
`getExamplePath()`	getExamplePath
`getFilledExampleDETha98Data()`	getFilledExampleDETha98Data
`getREddyProcExampleDir()`	getREddyProcExampleDir
`getStartRecsOfWindows()`	getStartRecsOfWindows
`getTZone()`	getTZone
`get_day_boundaries()`	get day boundaries
`get_timestep_hours()`	Get the timestep in fractional hours
`sID` `sDATA` `sINFO` `sLOCATION` `sTEMP` `sUSTAR`	globalDummyVars
`help_DateTimes()`	help DateTimes
`help_export()`	help export
`isValidNightRecord()`	compute logical vector of each rows in ds is its a valid night record
`partGLControl()`	partGLControl
`partGLControlLasslopCompatible()`	partGLControlLasslopCompatible
`partGLExtractStandardData()`	partGLExtractStandardData
`partGLFitLRCOneWindow()`	Estimate Rectangular Hyperbolic Light Response Curve parameters
`partGLFitLRCWindows()`	Estimate successive Rectangular Hyperbolic Light Response Curve parameters
`partGLInterpolateFluxes()`	Interpolate Reco and GPP from two neighboring parameter sets
`partGL_FitNight_1win_E0()`	Estimate temperature sensitivity E0 within one window
`partGL_FitNight_1win_E0_kernel()`	Estimate bounded temperature sensitivity E0 and RRef of ecosystem respiration
`partGL_FitNight_1win_RRef()`	Estimate Reference temperature from nighttime and given tempsens E0
`partGL_FitNight_E0_RRef()`	Partitioning of NEE into GPP and RE using the Lasslop et al. (2010) method
`partGL_smoothE0()`	Smoothes time development of E0
`partitionNEEGL()`	Partition NEE fluxes into GPP and Reco using the daytime method.
`%>%`	re-export magrittr pipe operator
`read_from_ameriflux22()`	Extract basic variables from Ameriflux standard (as of 2022) data.frames
`read_from_fluxnet15()`	extract REddyProc input columns from data.frame in Fluxnet15 format
`renameVariablesInDataframe()`	renameVariablesInDataframe
`replaceMissingSdByPercentage()`	replace missing standard deviation of a measure x by a percentage of x
`sEddyProc-class`	Class `"sEddyProc"`
`sEddyProc()`	sEddyProc
`sEddyProc_initialize()`	sEddyProc initialize
`sEddyProc_sApplyUStarScen()`	sEddyProc sApplyUStarScen
`sEddyProc_sCalcPotRadiation()`	sEddyProc sCalcPotRadiation
`sEddyProc_sEstUstarThold()`	sEddyProc$sEstUstarThreshold - Estimating ustar threshold
`sEddyProc_sEstUstarThreshold()`	sEddyProc$sEstUstarThreshold - Estimating ustar threshold
`sEddyProc_sEstUstarThresholdDistribution()`	sEddyProc sEstUstarThresholdDistribution
`sEddyProc_sEstimateUstarScenarios()`	sEddyProc sEstimateUstarScenarios
`sEddyProc_sExportData()`	sEddyProc sExportData
`sEddyProc_sExportResults()`	sEddyProc sExportResults
`sEddyProc_sFillInit()`	sEddyProc$sFillInit - Initialize gap filling
`sEddyProc_sFillLUT()`	sEddyProc sFillLUT
`sEddyProc_sFillMDC()`	sEddyProc sFillMDC
`sEddyProc_sFillVPDFromDew()`	Estimate VPD from daily minimum temperature
`sEddyProc_sGLFluxPartition()`	sEddyProc sGLFluxPartition
`sEddyProc_sGLFluxPartitionUStarScens()`	sEddyProc sGLFluxPartitionUStarScens
`sEddyProc_sGetData()`	sEddyProc sGetData
`sEddyProc_sGetEstimatedUstarThresholdDistribution()`	sEddyProc sGetEstimatedUstarThresholdDistribution
`sEddyProc_sGetUstarScenarios()`	sEddyProc sGetUstarScenarios
`sEddyProc_sGetUstarSuffixes()`	sEddyProc sGetUstarSuffixes
`sEddyProc_sMDSGapFill()`	sEddyProc sMDSGapFill
`sEddyProc_sMDSGapFillAfterUStarDistr()`	sEddyProc sMDSGapFillAfterUStarDistr
`sEddyProc_sMDSGapFillAfterUstar()`	sEddyProc sMDSGapFillAfterUstar
`sEddyProc_sMDSGapFillUStarScens()`	sEddyProc sMDSGapFillUStarScens
`sEddyProc_sMRFluxPartition()`	sEddyProc sMRFluxPartition
`sEddyProc_sMRFluxPartitionUStarScens()`	sEddyProc sMRFluxPartitionUStarScens
`sEddyProc_sPlotDailySums()`	sEddyProc$sPlotDailySums - Image with daily sums of each year
`sEddyProc_sPlotDailySumsY()`	sEddyProc sPlotDailySumsY
`sEddyProc_sPlotDiurnalCycle()`	sEddyProc sPlotDiurnalCycle
`sEddyProc_sPlotDiurnalCycleM()`	sEddyProc sPlotDiurnalCycleM
`sEddyProc_sPlotFingerprint()`	sEddyProc sPlotFingerprint
`sEddyProc_sPlotFingerprintY()`	sEddyProc sPlotFingerprintY
`sEddyProc_sPlotHHFluxes()`	sEddyProc sPlotHHFluxes
`sEddyProc_sPlotHHFluxesY()`	sEddyProc sPlotHHFluxesY
`sEddyProc_sPlotNEEVersusUStarForSeason()`	sEddyProc sPlotNEEVersusUStarForSeason
`sEddyProc_sSetLocationInfo()`	sEddyProc sSetLocationInfo
`sEddyProc_sSetUStarSeasons()`	sEddyProc sSetUStarSeasons
`sEddyProc_sSetUstarScenarios()`	sEddyProc sSetUstarScenarios
`sEddyProc_sTKFluxPartition()`	sEddyProc sTKFluxPartition
`sEddyProc_sTKFluxPartitionUStarScens()`	sEddyProc sTKFluxPartitionUStarScens
`sEddyProc_update_ustarthreshold_columns()`	Add columns reporting the uStar threshold for each scenario to sDATA
`sEddyProc_useAnnualUStarThresholds()`	sEddyProc useAnnualUStarThresholds
`sEddyProc_useSeaonsalUStarThresholds()`	sEddyProc useSeaonsalUStarThresholds
`simplifyApplyWindows()`	simplify the result returned by applyWindows
`usControlUstarEst()`	usControlUstarEst
`usControlUstarSubsetting()`	usControlUstarSubsetting
`usCreateSeasonFactorMonth()`	usCreateSeasonFactorMonth
`usCreateSeasonFactorMonthWithinYear()`	usCreateSeasonFactorMonthWithinYear
`usCreateSeasonFactorYday()`	usCreateSeasonFactorYday
`usCreateSeasonFactorYdayYear()`	usCreateSeasonFactorYdayYear
`usEstUstarThreshold()`	usEstUstarThreshold - Estimating ustar threshold
`usEstUstarThresholdSingleFw1Binned()`	usEstUstarThresholdSingleFw1Binned
`usEstUstarThresholdSingleFw2Binned()`	usEstUstarThresholdSingleFw2Binned
`usGetAnnualSeasonUStarMap()`	usGetAnnualSeasonUStarMap
`usGetSeasonalSeasonUStarMap()`	usGetSeasonalSeasonUStarMap
`usGetYearOfSeason()`	usGetYearOfSeason

Reference

All functions