├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── CRAN-SUBMISSION ├── DESCRIPTION ├── Dockerfile ├── NAMESPACE ├── NEWS.md ├── R ├── CheckVal.R ├── DataFunctions.R ├── EddyGapfilling.R ├── EddyPartitioning.R ├── EddyPlotting.R ├── EddyUStarFilterChangePointDetection.R ├── EddyUStarFilterDP.R ├── Example.R ├── FileHandling.R ├── FileHandlingFormats.R ├── GeoFunctions.R ├── LRC_base.R ├── LRC_logisticSigmoid.R ├── LRC_nonrectangular.R ├── LRC_rectangular.R ├── PartitioningLasslop10.R ├── PartitioningLasslop10Nighttime.R ├── RcppExports.R ├── aEddy.R ├── estimate_vpd_from_dew.R ├── imports.R ├── logitnorm.R ├── variableNames.R └── zzzDebugCode.R ├── README-example-1.png ├── README.Rmd ├── README.md ├── cran-comments.md ├── data ├── DEGebExample.RData └── Example_DETha98.RData ├── develop ├── DevelopmentNotes.docx ├── FlowDiagramGapfilling.pptx ├── MDSFlow.jpg ├── OutputColsExample.xlsx ├── compOldNewTool.R ├── compareOldTool │ ├── EvaluationGLPartitioning.R │ ├── EvaluationGLPartitioning_debug.R │ ├── GLPartitioningTestCase.R │ ├── GlParitioningTestCasePlots.R │ ├── HarvardForestCase.R │ ├── TharandtCase.R │ └── compare_NRect.R ├── debug_dump_rda.R ├── debug_onlineTool.R ├── dockerCran │ ├── Dockerfile │ └── readme.txt ├── dockerDepends │ └── Dockerfile ├── dockerSuggests │ └── Dockerfile ├── genDEGebExample.R ├── genOldToolData.R ├── genRpackage.R ├── partGL_ControlFlow.graphml ├── partGL_ControlFlow.pdf ├── profile │ ├── profile.R │ └── readme.md ├── setREnvir.R ├── templateInlinedocs.R └── testEddyProc.R ├── examples ├── Example_DE-Tha.1996.1998.hourly_selVars.nc ├── Example_DETha98.txt └── readme.txt ├── inst ├── .gitignore ├── WORDLIST ├── examples │ ├── .gitignore │ ├── Example_DE-Tha.1996.1998.hourly_selVars.nc │ └── Example_DETha98.txt └── genData │ ├── DEGebExample.Rd │ ├── Example_DETha98.Rd │ ├── LightResponseCurveFitter-class.Rd │ ├── LightResponseCurveFitter.Rd │ ├── LogisticSigmoidLRCFitter-class.Rd │ ├── LogisticSigmoidLRCFitter.Rd │ ├── NonrectangularLRCFitter-class.Rd │ ├── NonrectangularLRCFitter.Rd │ ├── REddyProc-package.Rd │ ├── RHLightResponseCostC.Rd │ ├── RectangularLRCFitter-class.Rd │ ├── RectangularLRCFitter.Rd │ ├── RectangularLRCFitterCVersion-class.Rd │ ├── RectangularLRCFitterCVersion.Rd │ ├── deleteRdList.txt │ ├── globalDummyVars.Rd │ ├── pipe.Rd │ ├── sEddyProc-class.Rd │ └── sEddyProc.Rd ├── man ├── BerkeleyJulianDateToPOSIXct.Rd ├── DEGebExample.Rd ├── Example_DETha98.Rd ├── LightResponseCurveFitter-class.Rd ├── LightResponseCurveFitter.Rd ├── LightResponseCurveFitter_computeCost.Rd ├── LightResponseCurveFitter_computeLRCGradient.Rd ├── LightResponseCurveFitter_fitLRC.Rd ├── LightResponseCurveFitter_getOptimizedParameterPositions.Rd ├── LightResponseCurveFitter_getParameterInitials.Rd ├── LightResponseCurveFitter_getParameterNames.Rd ├── LightResponseCurveFitter_getPriorLocation.Rd ├── LightResponseCurveFitter_getPriorScale.Rd ├── LightResponseCurveFitter_isParameterInBounds.Rd ├── LightResponseCurveFitter_optimLRC.Rd ├── LightResponseCurveFitter_optimLRCBounds.Rd ├── LightResponseCurveFitter_optimLRCOnAdjustedPrior.Rd ├── LightResponseCurveFitter_predictGPP.Rd ├── LightResponseCurveFitter_predictLRC.Rd ├── LogisticSigmoidLRCFitter-class.Rd ├── LogisticSigmoidLRCFitter.Rd ├── LogisticSigmoidLRCFitter_predictGPP.Rd ├── NonrectangularLRCFitter-class.Rd ├── NonrectangularLRCFitter.Rd ├── NonrectangularLRCFitter_getParameterNames.Rd ├── NonrectangularLRCFitter_predictGPP.Rd ├── POSIXctToBerkeleyJulianDate.Rd ├── REddyProc-package.Rd ├── REddyProc_defaultunits.Rd ├── RHLightResponseCostC.Rd ├── RectangularLRCFitter-class.Rd ├── RectangularLRCFitter.Rd ├── RectangularLRCFitterCVersion-class.Rd ├── RectangularLRCFitterCVersion.Rd ├── RectangularLRCFitter_predictGPP.Rd ├── estimate_vpd_from_dew.Rd ├── extract_FN15.Rd ├── fCalcAVPfromVMFandPress.Rd ├── fCalcETfromLE.Rd ├── fCalcExtRadiation.Rd ├── fCalcPotRadiation.Rd ├── fCalcRHfromAVPandTair.Rd ├── fCalcSVPfromTair.Rd ├── fCalcVPDfromRHandTair.Rd ├── fCheckHHTimeSeries.Rd ├── fConvertCtoK.Rd ├── fConvertGlobalToVisible.Rd ├── fConvertKtoC.Rd ├── fConvertTimeToPosix.Rd ├── fConvertVisibleWm2toPhotons.Rd ├── fKeepColumnAttributes.Rd ├── fLloydTaylor.Rd ├── fLoadAmeriflux22.Rd ├── fLoadEuroFlux16.Rd ├── fLoadFluxnet15.Rd ├── fLoadTXTIntoDataframe.Rd ├── fSplitDateTime.Rd ├── fWriteDataframeToFile.Rd ├── fWriteFrench23.Rd ├── filterLongRuns.Rd ├── filterLongRunsInVector.Rd ├── filter_entire_days.Rd ├── filter_years_eop.Rd ├── getAmerifluxToBGC05VariableNameMapping.Rd ├── getBGC05ToAmerifluxVariableNameMapping.Rd ├── getExamplePath.Rd ├── getFilledExampleDETha98Data.Rd ├── getREddyProcExampleDir.Rd ├── getTZone.Rd ├── get_day_boundaries.Rd ├── get_timestep_hours.Rd ├── globalDummyVars.Rd ├── help_DateTimes.Rd ├── help_export.Rd ├── partGLControl.Rd ├── partGLControlLasslopCompatible.Rd ├── partGLExtractStandardData.Rd ├── partitionNEEGL.Rd ├── pipe.Rd ├── read_from_ameriflux22.Rd ├── read_from_fluxnet15.Rd ├── renameVariablesInDataframe.Rd ├── sEddyProc-class.Rd ├── sEddyProc.Rd ├── sEddyProc_initialize.Rd ├── sEddyProc_sApplyUStarScen.Rd ├── sEddyProc_sCalcPotRadiation.Rd ├── sEddyProc_sEstUstarThold.Rd ├── sEddyProc_sEstUstarThreshold.Rd ├── sEddyProc_sEstUstarThresholdDistribution.Rd ├── sEddyProc_sEstimateUstarScenarios.Rd ├── sEddyProc_sExportData.Rd ├── sEddyProc_sExportResults.Rd ├── sEddyProc_sFillInit.Rd ├── sEddyProc_sFillLUT.Rd ├── sEddyProc_sFillMDC.Rd ├── sEddyProc_sFillVPDFromDew.Rd ├── sEddyProc_sGLFluxPartition.Rd ├── sEddyProc_sGLFluxPartitionUStarScens.Rd ├── sEddyProc_sGetData.Rd ├── sEddyProc_sGetEstimatedUstarThresholdDistribution.Rd ├── sEddyProc_sGetUstarScenarios.Rd ├── sEddyProc_sGetUstarSuffixes.Rd ├── sEddyProc_sMDSGapFill.Rd ├── sEddyProc_sMDSGapFillAfterUStarDistr.Rd ├── sEddyProc_sMDSGapFillAfterUstar.Rd ├── sEddyProc_sMDSGapFillUStarScens.Rd ├── sEddyProc_sMRFluxPartition.Rd ├── sEddyProc_sMRFluxPartitionUStarScens.Rd ├── sEddyProc_sPlotDailySums.Rd ├── sEddyProc_sPlotDailySumsY.Rd ├── sEddyProc_sPlotDiurnalCycle.Rd ├── sEddyProc_sPlotDiurnalCycleM.Rd ├── sEddyProc_sPlotFingerprint.Rd ├── sEddyProc_sPlotFingerprintY.Rd ├── sEddyProc_sPlotHHFluxes.Rd ├── sEddyProc_sPlotHHFluxesY.Rd ├── sEddyProc_sPlotNEEVersusUStarForSeason.Rd ├── sEddyProc_sSetLocationInfo.Rd ├── sEddyProc_sSetUStarSeasons.Rd ├── sEddyProc_sSetUstarScenarios.Rd ├── sEddyProc_sTKFluxPartition.Rd ├── sEddyProc_sTKFluxPartitionUStarScens.Rd ├── sEddyProc_update_ustarthreshold_columns.Rd ├── sEddyProc_useAnnualUStarThresholds.Rd ├── sEddyProc_useSeasonalUStarThresholds.Rd ├── usControlUstarEst.Rd ├── usControlUstarSubsetting.Rd ├── usCreateSeasonFactorMonth.Rd ├── usCreateSeasonFactorMonthWithinYear.Rd ├── usCreateSeasonFactorYday.Rd ├── usCreateSeasonFactorYdayYear.Rd ├── usEstUstarThreshold.Rd ├── usEstUstarThresholdSingleFw1Binned.Rd ├── usEstUstarThresholdSingleFw2Binned.Rd ├── usGetAnnualSeasonUStarMap.Rd ├── usGetSeasonalSeasonUStarMap.Rd └── usGetYearOfSeason.Rd ├── revdep ├── .gitignore └── email.yml ├── src ├── RHLightResponseCostC.cpp ├── RcppExports.cpp └── whichValueGreaterEqualC.cpp ├── tests ├── doRUnit.R └── testthat │ ├── .gitignore │ ├── test_FileHandlingFormats.R │ ├── test_LightResponseCurveFitter.R │ ├── test_UStarFilter.R │ ├── test_binWithEqualValues.R │ ├── test_checkval.R │ ├── test_estimate_vpd_from_dew.R │ ├── test_fCheckValue.R │ ├── test_fConvertTimeToPosix.R │ ├── test_gapfilling.R │ ├── test_geoFunctions.R │ ├── test_getExamplePath.R │ ├── test_partGL.R │ ├── test_plotFingerprint.R │ ├── test_sEddyProc.R │ ├── test_sEddyProc_Partitioning.R │ └── test_uStarProc.R └── vignettes ├── DEGebExample.Rmd ├── DEGebExample.md ├── DEGebExample_files ├── figure-html │ └── DEGeb_estUStar1a-1.png └── figure-markdown_strict │ └── DEGeb_estUStar1a-1.png ├── 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