REddyProc: Data processing and plotting utilities of (half-)hourly eddy-covariance measurements
Version 1.0.0

R eddy processing package with MDS gap filling algorithm, adopted after PV-Wave source code from Markus Reichstein.

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Author(Department for Biogeochemical Integration at MPI-BGC, Jena, Germany)
Date of publication2017-03-13 07:30:41
MaintainerDepartment for Biogeochemical Integration <REddyProc-help@bgc.mpg.de>
LicenseGPL (>= 2)
Version1.0.0
URL http://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb http://r-forge.r-project.org/projects/reddyproc/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("REddyProc", repos="http://R-Forge.R-project.org")

Man pages

applyWindows: applyWindows
BerkeleyJulianDateToPOSIXct: BerkeleyJulianDateToPOSIXct
DEGebExample: Eddy covariance data from Gebesee crop site, Germany
Example_DETha98: Eddy covariance data from Tharandt, Germany
fAddNCFVar: fAddNCFVar
fCalcAVPfromVMFandPress: fCalcAVPfromVMFandPress
fCalcETfromLE: fCalcETfromLE
fCalcExtRadiation: fCalcExtRadiation
fCalcLengthOfGaps: fCalcLengthOfGaps
fCalcPotRadiation: fCalcPotRadiation
fCalcRHfromAVPandTair: fCalcRHfromAVPandTair
fCalcSunPosition: fCalcSunPosition
fCalcSVPfromTair: fCalcSVPfromTair
fCalcVPDfromRHandTair: fCalcVPDfromRHandTair
fCheckColNames: fCheckColNames
fCheckColNum: fCheckColNum
fCheckColPlausibility: fCheckColPlausibility
fCheckHHTimeSeries: fCheckHHTimeSeries
fCheckOutsideRange: fCheckOutsideRange
fCheckValNum: fCheckValNum
fCheckValString: fCheckValString
fConvertCtoK: fConvertCtoK
fConvertGapsToNA: fConvertGapsToNA
fConvertGlobalToVisible: fConvertGlobalToVisible
fConvertKtoC: fConvertKtoC
fConvertNAsToGap: fConvertNAsToGap
fConvertTimeToPosix: Convert different time formats to POSIX
fConvertVisibleWm2toPhotons: fConvertVisibleWm2toPhotons
fExpandToFullYear: fExpandToFullYear
fFilterAttr: fFilterAttr
fFullYearTimeSteps: fFullYearTimeSteps
fGetBeginOfEddyPeriod: fGetBeginOfEddyPeriod
fGetEndOfEddyPeriod: fGetEndOfEddyPeriod
fGetYearOfEddyPeriod: fGetYearOfEddyPeriod
fillNAForward: fillNAForward
fInitFilesDir: fInitFilesDir
fInterpolateGaps: fInterpolateGaps
fLloydTaylor: Temperature dependence of soil respiration
fLoadEuroFlux16: fLoadEuroFlux16
fLoadFluxNCInfo: Get site information from BGI NetCDF files
fLoadFluxNCIntoDataframe: Load NetCDF file
fLoadTXTIntoDataframe: Load text file with one header and one unit row into data...
fOptimSingleE0: Estimate temperature sensitivity E_0 using a Newton type...
fOptimSingleE0_Lev: Estimate temperature sensitivity E_0 using Levenberg-Marquard...
fReadTimeBerkeley: fReadTimeBerkeley
fReadTimeSeveralCols: fReadTimeSeveralCols
fRegrE0fromShortTerm: Estimation of the temperature sensitivity E_0
fSetFile: fSetFile
fSetQF: Check and set quality flag
fStripFileExtension: fStripFileExtension
fWriteDataframeToFile: fWriteDataframeToFile
getAmerifluxToBGC05VariableNameMapping: getAmerifluxToBGC05VariableNameMapping
getBGC05ToAmerifluxVariableNameMapping: getBGC05ToAmerifluxVariableNameMapping
isValidNightRecord: isValidNightRecord
parmGLOptimLRCBounds: parmGLOptimLRCBounds
partGLBoundParameters: partGLBoundParameters
partGLControl: partGLControl
partGLEstimateTempSensInBoundsE0Only: partGLEstimateTempSensInBoundsE0Only
partGLFitLRC: partGLFitLRC
partGLFitLRCOneWindow: partGLFitLRCOneWindow
partGLFitLRCWindows: partGLFitLRCWindows
partGLFitNightRespRefOneWindow: partGLFitNightRespRefOneWindow
partGLFitNightTempSensOneWindow: partGLFitNightTempSensOneWindow
partGLInterpolateFluxes: partGLInterpolateFluxes
partGL_RHLightResponse: partGL RHLightResponse
partGL_RHLightResponseGrad: partGL RHLightResponseGrad
partGLSmoothTempSens: partGLSmoothTempSens
partitionNEEGL: partitionNEEGL
POSIXctToBerkeleyJulianDate: POSIXctToBerkeleyJulianDate
REddyProc-package: Data processing and plotting utilities of (half-)hourly...
renameVariablesInDataframe: renameVariablesInDataframe
RHLightResponseCostC: RHLightResponseCostC
sCalcPotRadiation: sCalcPotRadiation
sEddyProc.example: sEddyProc - Example code
sEddyProc.new: sEddyProc$new - Initialization of sEddyProc
sEstUstarThreshold: sEddyProc$sEstUstarThreshold - Estimating ustar threshold
sEstUstarThresholdDistribution: sEstUstarThresholdDistribution
sExportData: sEddyProc$sExportData - Export internal sDATA data frame
sExportResults: sEddyProc$sExportData - Export internal sTEMP data frame with...
sFillInit: sEddyProc$sFillInit - Initialize gap filling
sFillLUT: sEddyProc$sFillLUT - Gap filling with Look-Up Table (LUT)
sFillMDC: sEddyProc$sFillMDC - Gap filling with Mean Diurnal Course...
sGetData: sEddyProc$sGetData - Get internal sDATA data frame
sGLFluxPartition: sGLFluxPartition: Flux partitioning after Lasslop et al....
sMDSGapFill: sEddyProc$sMDSGapFill - MDS gap filling algorithm
sMDSGapFillAfterUstar: sEddyProc$sMDSGapFillAfterUstar - MDS gap filling algorithm...
sMDSGapFillAfterUStarDistr: GapFilling for several filters of estimated friction velocity...
sMRFluxPartition: sEddyProc$sMRFluxPartition - Flux partitioning after...
sPlotDailySums: sEddyProc$sPlotDailySums - Image with daily sums of each year
sPlotDailySumsY: sEddyProc$sPlotDailySumsY - Plot daily sum of specified year
sPlotDiurnalCycle: sEddyProc$sPlotDiurnalCycle - Image with diurnal cycles of...
sPlotFingerprint: sEddyProc$sPlotFingerprint - Image with fingerprints of each...
sPlotFingerprintY: sEddyProc$sPlotFingerprintY - Plot fingerprint of specified...
sPlotHHFluxes: sEddyProc$sPlotHHFluxes - Image with half-hourly fluxes for...
sPlotHHFluxesY: sEddyProc$sPlotHHFluxesY - Plot half-hourly fluxes of...
sPlotNEEVersusUStarForSeason: sEddyProc$sPlotNEEVersusUStarForSeason - Image with NEE...
sPrintFrames: sEddyProc$sPrintFrames - Print internal sDATA and sTEMP data...
sRegrE0fromShortTerm: sEddyProc$sRegrE0fromShortTerm - Estimation of the...
sRegrRref: sEddyProc$sRegrRref - Estimation of the time series of...
sSetLocationInfo: sSetLocationInfo
usControlUstarEst: usControlUstarEst
usControlUstarSubsetting: usControlUstarSubsetting
usCreateSeasonFactorMonth: usCreateSeasonFactorMonth
usCreateSeasonFactorMonthWithinYear: usCreateSeasonFactorMonthWithinYear
usCreateSeasonFactorYday: usCreateSeasonFactorYday
usCreateSeasonFactorYdayYear: usCreateSeasonFactorYdayYear
usEstUstarThreshold: usEstUstarThreshold - Estimating ustar threshold
usEstUstarThresholdSingleFw1Binned: usEstUstarThresholdSingleFw1Binned
usEstUstarThresholdSingleFw2Binned: usEstUstarThresholdSingleFw2Binned
usGetAnnualSeasonUStarMappingFromDistributionResult: usGetAnnualSeasonUStarMappingFromDistributionResult
usGetSeaonalSeasonUStarMappingFromDistributionResult: usGetSeaonalSeasonUStarMappingFromDistributionResult
usGetSeasonalSeasonUStarMappingFromDistributionResult: usGetSeasonalSeasonUStarMappingFromDistributionResult
usGetValidUstarIndices: usGetValidUstarIndices
usGetYearOfSeason: usGetYearOfSeason
whichValueGreaterEqualC: whichValueGreaterEqualC

Functions

BerkeleyJulianDateToPOSIXct Man page Source code
DEGebExample Man page
Example_DETha98 Man page
POSIXctToBerkeleyJulianDate Man page Source code
REddyProc Man page
REddyProc-package Man page
RHLightResponseCostC Man page Source code
applyWindows Man page Source code
binUstar Source code
binWithEqualValuesBalanced Source code
binWithEqualValuesMinRec Source code
bootStrapLRCFit Source code
estimateUStarSeason Source code
estimateUStarSeasonCPTSeveralT Source code
fAddNCFVar Man page Source code
fCalcAVPfromVMFandPress Man page Source code
fCalcETfromLE Man page Source code
fCalcExtRadiation Man page Source code
fCalcLengthOfGaps Man page Source code
fCalcPotRadiation Man page Source code
fCalcRHfromAVPandTair Man page Source code
fCalcSVPfromTair Man page Source code
fCalcSunPosition Man page Source code
fCalcVPDfromRHandTair Man page Source code
fCheckColNames Man page Source code
fCheckColNum Man page Source code
fCheckColPlausibility Man page Source code
fCheckHHTimeSeries Man page Source code
fCheckOutsideRange Man page Source code
fCheckValNum Man page Source code
fCheckValString Man page Source code
fConvertCtoK Man page Source code
fConvertGapsToNA Man page Source code
fConvertGlobalToVisible Man page Source code
fConvertKtoC Man page Source code
fConvertNAsToGap Man page Source code
fConvertTimeToPosix Man page Source code
fConvertVisibleWm2toPhotons Man page Source code
fExpandToFullYear Man page Source code
fFilterAttr Man page Source code
fFullYearTimeSteps Man page Source code
fGetBeginOfEddyPeriod Man page Source code
fGetEndOfEddyPeriod Man page Source code
fGetYearOfEddyPeriod Man page Source code
fInitFilesDir Man page Source code
fInterpolateGaps Man page Source code
fLloydTaylor Man page Source code
fLoadEuroFlux16 Man page Source code
fLoadFluxNCInfo Man page Source code
fLoadFluxNCIntoDataframe Man page Source code
fLoadTXTIntoDataframe Man page Source code
fOptimSingleE0 Man page Source code
fOptimSingleE0_Lev Man page Source code
fReadTimeBerkeley Man page Source code
fReadTimeSeveralCols Man page Source code
fRegrE0fromShortTerm Man page Source code
fSetFile Man page Source code
fSetQF Man page Source code
fStripFileExtension Man page Source code
fWriteDataframeToFile Man page Source code
fillNAForward Man page Source code
fitSeg1 Source code
fitSeg2 Source code
getAmerifluxToBGC05VariableNameMapping Man page Source code
getBGC05ToAmerifluxVariableNameMapping Man page Source code
isValidNightRecord Man page Source code
optimLRC Source code
parmGLOptimLRCBounds Man page Source code
partGLBoundParameters Man page Source code
partGLControl Man page Source code
partGLEstimateTempSensInBoundsE0Only Man page Source code
partGLFitLRC Man page Source code
partGLFitLRCOneWindow Man page Source code
partGLFitLRCWindows Man page Source code
partGLFitNightRespRefOneWindow Man page Source code
partGLFitNightTempSensOneWindow Man page Source code
partGLInterpolateFluxes Man page Source code
partGLRHLightResponseCost Source code
partGLRHLightResponseCostLogBeta Source code
partGLSmoothTempSens Man page Source code
partGL_RHLightResponse Man page Source code
partGL_RHLightResponseGrad Man page Source code
partGPAssociateSpecialRows Source code
partitionNEEGL Man page Source code
plotNEEVersusUStarTempClass Source code
renameVariablesInDataframe Man page Source code
sCalcPotRadiation Man page
sEddyProc.example Man page Source code
sEddyProc.new Man page
sEstUstarThreshold Man page
sEstUstarThresholdDistribution Man page
sExportData Man page
sExportResults Man page
sFillInit Man page
sFillLUT Man page
sFillMDC Man page
sGLFluxPartition Man page
sGetData Man page
sMDSGapFill Man page
sMDSGapFillAfterUStarDistr Man page
sMDSGapFillAfterUstar Man page
sMRFluxPartition Man page
sPlotDailySums Man page
sPlotDailySumsY Man page
sPlotDiurnalCycle Man page
sPlotFingerprint Man page
sPlotFingerprintY Man page
sPlotHHFluxes Man page
sPlotHHFluxesY Man page
sPlotNEEVersusUStarForSeason Man page
sPrintFrames Man page
sRegrE0fromShortTerm Man page
sRegrRref Man page
sSetLocationInfo Man page
tmp.f Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
usControlUstarEst Man page Source code
usControlUstarSubsetting Man page Source code
usCreateSeasonFactorMonth Man page Source code
usCreateSeasonFactorMonthWithinYear Man page Source code
usCreateSeasonFactorYday Man page Source code
usCreateSeasonFactorYdayYear Man page Source code
usEstUstarThreshold Man page Source code
usEstUstarThresholdSingleFw1Binned Man page Source code
usEstUstarThresholdSingleFw2Binned Man page Source code
usGetAnnualSeasonUStarMappingFromDistributionResult Man page Source code
usGetSeaonalSeasonUStarMappingFromDistributionResult Man page
usGetSeasonalSeasonUStarMappingFromDistributionResult Man page
usGetValidUstarIndices Man page Source code
usGetYearOfSeason Man page Source code
whichValueGreaterEqual Source code
whichValueGreaterEqualC Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS.md
R
R/DataFunctions.R
R/Eddy.R
R/EddyGapfilling.R
R/EddyPartitioning.R
R/EddyPlotting.R
R/EddyUStarFilterChangePointDetection.R
R/EddyUStarFilterDP.R
R/Example.R
R/FileHandling.R
R/FileHandlingFormats.R
R/GeoFunctions.R
R/PartitioningLasslop10.R
R/RcppExports.R
R/cFunc.R
R/variableNames.R
R/zzzDebugCode.R
build
build/vignette.rds
data
data/DEGebExample.RData
data/Example_DETha98.RData
data/datalist
inst
inst/compareOldTool
inst/compareOldTool/EvaluationGLPartitioning.R
inst/compareOldTool/HarvardForestCase.R
inst/compareOldTool/TharandtCase.R
inst/develop
inst/develop/DevelopmentNotes.docx
inst/develop/FlowDiagramGapfilling.pptx
inst/develop/MDSFlow.jpg
inst/develop/OutputColsExample.xlsx
inst/develop/compOldNewTool.R
inst/develop/genDEGebExample.R
inst/develop/genDocu
inst/develop/genDocu/DEGebExample.Rd
inst/develop/genDocu/Example_DETha98.Rd
inst/develop/genDocu/REddyProc-package.Rd
inst/develop/genOldToolData.R
inst/develop/genRpackage.R
inst/develop/partGL_ControlFlow.graphml
inst/develop/partGL_ControlFlow.pdf
inst/develop/setREnvir.R
inst/develop/templateInlinedocs.R
inst/develop/testEddyProc.R
inst/doc
inst/doc/DEGebExample.Rmd
inst/doc/DEGebExample.html
inst/examples
inst/examples/Example_DE-Tha.1996.1998.hourly.nc
inst/examples/Example_DETha98.txt
inst/examples/Example_DETha98_PVWave_DataSetafterFluxpart.txt
inst/examples/PVWave_TH98_new.txt
inst/scripts
inst/scripts/DataFunctions.R
inst/scripts/Eddy.R
inst/scripts/EddyGapfilling.R
inst/scripts/EddyPartitioning.R
inst/scripts/EddyPlotting.R
inst/scripts/EddyUStarFilterChangePointDetection.R
inst/scripts/EddyUStarFilterDP.R
inst/scripts/Example.R
inst/scripts/FileHandling.R
inst/scripts/FileHandlingFormats.R
inst/scripts/GeoFunctions.R
inst/scripts/RcppExports.R
inst/scripts/cFunc.R
inst/scripts/variableNames.R
inst/scripts/zzzDebugCode.R
inst/tests
inst/tests/test_UStarFilter.R
inst/tests/test_binWithEqualValues.R
inst/tests/test_fCalcPotRadiation.R
inst/tests/test_fCheckValue.R
inst/tests/test_fConvertTimeToPosix.R
inst/tests/test_fileHandling.R
inst/tests/test_partGL.R
inst/tests/test_sEddyProc.R
inst/tests/test_sEddyProc_Partitioning.R
inst/tests2
inst/tests2/test_readNcdf.R
man
man/BerkeleyJulianDateToPOSIXct.Rd
man/DEGebExample.Rd
man/Example_DETha98.Rd
man/POSIXctToBerkeleyJulianDate.Rd
man/REddyProc-package.Rd
man/RHLightResponseCostC.Rd
man/applyWindows.Rd
man/fAddNCFVar.Rd
man/fCalcAVPfromVMFandPress.Rd
man/fCalcETfromLE.Rd
man/fCalcExtRadiation.Rd
man/fCalcLengthOfGaps.Rd
man/fCalcPotRadiation.Rd
man/fCalcRHfromAVPandTair.Rd
man/fCalcSVPfromTair.Rd
man/fCalcSunPosition.Rd
man/fCalcVPDfromRHandTair.Rd
man/fCheckColNames.Rd
man/fCheckColNum.Rd
man/fCheckColPlausibility.Rd
man/fCheckHHTimeSeries.Rd
man/fCheckOutsideRange.Rd
man/fCheckValNum.Rd
man/fCheckValString.Rd
man/fConvertCtoK.Rd
man/fConvertGapsToNA.Rd
man/fConvertGlobalToVisible.Rd
man/fConvertKtoC.Rd
man/fConvertNAsToGap.Rd
man/fConvertTimeToPosix.Rd
man/fConvertVisibleWm2toPhotons.Rd
man/fExpandToFullYear.Rd
man/fFilterAttr.Rd
man/fFullYearTimeSteps.Rd
man/fGetBeginOfEddyPeriod.Rd
man/fGetEndOfEddyPeriod.Rd
man/fGetYearOfEddyPeriod.Rd
man/fInitFilesDir.Rd
man/fInterpolateGaps.Rd
man/fLloydTaylor.Rd
man/fLoadEuroFlux16.Rd
man/fLoadFluxNCInfo.Rd
man/fLoadFluxNCIntoDataframe.Rd
man/fLoadTXTIntoDataframe.Rd
man/fOptimSingleE0.Rd
man/fOptimSingleE0_Lev.Rd
man/fReadTimeBerkeley.Rd
man/fReadTimeSeveralCols.Rd
man/fRegrE0fromShortTerm.Rd
man/fSetFile.Rd
man/fSetQF.Rd
man/fStripFileExtension.Rd
man/fWriteDataframeToFile.Rd
man/fillNAForward.Rd
man/getAmerifluxToBGC05VariableNameMapping.Rd
man/getBGC05ToAmerifluxVariableNameMapping.Rd
man/isValidNightRecord.Rd
man/parmGLOptimLRCBounds.Rd
man/partGLBoundParameters.Rd
man/partGLControl.Rd
man/partGLEstimateTempSensInBoundsE0Only.Rd
man/partGLFitLRC.Rd
man/partGLFitLRCOneWindow.Rd
man/partGLFitLRCWindows.Rd
man/partGLFitNightRespRefOneWindow.Rd
man/partGLFitNightTempSensOneWindow.Rd
man/partGLInterpolateFluxes.Rd
man/partGLSmoothTempSens.Rd
man/partGL_RHLightResponse.Rd
man/partGL_RHLightResponseGrad.Rd
man/partitionNEEGL.Rd
man/renameVariablesInDataframe.Rd
man/sCalcPotRadiation.Rd
man/sEddyProc.example.Rd
man/sEddyProc.new.Rd
man/sEstUstarThreshold.Rd
man/sEstUstarThresholdDistribution.Rd
man/sExportData.Rd
man/sExportResults.Rd
man/sFillInit.Rd
man/sFillLUT.Rd
man/sFillMDC.Rd
man/sGLFluxPartition.Rd
man/sGetData.Rd
man/sMDSGapFill.Rd
man/sMDSGapFillAfterUStarDistr.Rd
man/sMDSGapFillAfterUstar.Rd
man/sMRFluxPartition.Rd
man/sPlotDailySums.Rd
man/sPlotDailySumsY.Rd
man/sPlotDiurnalCycle.Rd
man/sPlotFingerprint.Rd
man/sPlotFingerprintY.Rd
man/sPlotHHFluxes.Rd
man/sPlotHHFluxesY.Rd
man/sPlotNEEVersusUStarForSeason.Rd
man/sPrintFrames.Rd
man/sRegrE0fromShortTerm.Rd
man/sRegrRref.Rd
man/sSetLocationInfo.Rd
man/usControlUstarEst.Rd
man/usControlUstarSubsetting.Rd
man/usCreateSeasonFactorMonth.Rd
man/usCreateSeasonFactorMonthWithinYear.Rd
man/usCreateSeasonFactorYday.Rd
man/usCreateSeasonFactorYdayYear.Rd
man/usEstUstarThreshold.Rd
man/usEstUstarThresholdSingleFw1Binned.Rd
man/usEstUstarThresholdSingleFw2Binned.Rd
man/usGetAnnualSeasonUStarMappingFromDistributionResult.Rd
man/usGetSeaonalSeasonUStarMappingFromDistributionResult.Rd
man/usGetSeasonalSeasonUStarMappingFromDistributionResult.Rd
man/usGetValidUstarIndices.Rd
man/usGetYearOfSeason.Rd
man/whichValueGreaterEqualC.Rd
src
src/RHLightResponseCostC.cpp
src/RcppExports.cpp
src/whichValueGreaterEqualC.cpp
tests
tests/doRUnit.R
vignettes
vignettes/DEGebExample.Rmd
REddyProc documentation built on May 21, 2017, 1:12 a.m.