Package: REddyProc 1.3.3

REddyProc: Post Processing of (Half-)Hourly Eddy-Covariance Measurements

Standard and extensible Eddy-Covariance data post-processing (Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>) includes uStar-filtering, gap-filling, and flux-partitioning. The Eddy-Covariance (EC) micrometeorological technique quantifies continuous exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere. It is important for understanding ecosystem dynamics and upscaling exchange fluxes. (Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>). This package inputs pre-processed (half-)hourly data and supports further processing. First, a quality-check and filtering is performed based on the relationship between measured flux and friction velocity (uStar) to discard biased data (Papale et al. (2006) <doi:10.5194/bg-3-571-2006>). Second, gaps in the data are filled based on information from environmental conditions (Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>). Third, the net flux of carbon dioxide is partitioned into its gross fluxes in and out of the ecosystem by night-time based and day-time based approaches (Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).

Authors:Department for Biogeochemical Integration at MPI-BGC, Jena, Germany [cph], Thomas Wutzler [aut, cre], Markus Reichstein [aut], Antje Maria Moffat [aut, trl], Olaf Menzer [ctb], Mirco Migliavacca [aut], Kerstin Sickel [ctb, trl], Ladislav <U+0160>igut [ctb]

REddyProc_1.3.3.tar.gz
REddyProc_1.3.3.zip(r-4.5)REddyProc_1.3.3.zip(r-4.4)REddyProc_1.3.3.zip(r-4.3)
REddyProc_1.3.3.tgz(r-4.4-x86_64)REddyProc_1.3.3.tgz(r-4.4-arm64)REddyProc_1.3.3.tgz(r-4.3-x86_64)REddyProc_1.3.3.tgz(r-4.3-arm64)
REddyProc_1.3.3.tar.gz(r-4.5-noble)REddyProc_1.3.3.tar.gz(r-4.4-noble)
REddyProc_1.3.3.tgz(r-4.4-emscripten)REddyProc_1.3.3.tgz(r-4.3-emscripten)
REddyProc.pdf |REddyProc.html
REddyProc/json (API)
NEWS

# Install 'REddyProc' in R:
install.packages('REddyProc', repos = c('https://bgctw.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bgctw/reddyproc/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

cpp

10.95 score 58 stars 16 packages 158 scripts 1.4k downloads 6 mentions 127 exports 36 dependencies

Last updated 14 days agofrom:97591553e7. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 25 2024
R-4.5-win-x86_64NOTENov 25 2024
R-4.5-linux-x86_64NOTENov 25 2024
R-4.4-win-x86_64OKNov 25 2024
R-4.4-mac-x86_64OKNov 25 2024
R-4.4-mac-aarch64OKNov 25 2024
R-4.3-win-x86_64OKNov 25 2024
R-4.3-mac-x86_64OKNov 25 2024
R-4.3-mac-aarch64OKNov 25 2024

Exports:%>%BerkeleyJulianDateToPOSIXctestimate_vpd_from_dewextract_FN15fCalcAVPfromVMFandPressfCalcETfromLEfCalcExtRadiationfCalcPotRadiationfCalcRHfromAVPandTairfCalcSVPfromTairfCalcVPDfromRHandTairfCheckHHTimeSeriesfConvertCtoKfConvertGlobalToVisiblefConvertKtoCfConvertTimeToPosixfConvertVisibleWm2toPhotonsfilter_entire_daysfilter_years_eopfilterLongRunsfilterLongRunsInVectorfKeepColumnAttributesfLloydTaylorfLoadAmeriflux22fLoadEuroFlux16fLoadFluxnet15fLoadTXTIntoDataframefSplitDateTimefWriteDataframeToFilefWriteFrench23get_day_boundariesget_timestep_hoursgetAmerifluxToBGC05VariableNameMappinggetBGC05ToAmerifluxVariableNameMappinggetExamplePathgetFilledExampleDETha98DatagetREddyProcExampleDirgetTZonehelp_DateTimeshelp_exportLightResponseCurveFitterLightResponseCurveFitter_computeCostLightResponseCurveFitter_computeLRCGradientLightResponseCurveFitter_fitLRCLightResponseCurveFitter_getOptimizedParameterPositionsLightResponseCurveFitter_getParameterInitialsLightResponseCurveFitter_getParameterNamesLightResponseCurveFitter_getPriorLocationLightResponseCurveFitter_getPriorScaleLightResponseCurveFitter_isParameterInBoundsLightResponseCurveFitter_optimLRCLightResponseCurveFitter_optimLRCBoundsLightResponseCurveFitter_optimLRCOnAdjustedPriorLightResponseCurveFitter_predictGPPLightResponseCurveFitter_predictLRCLogisticSigmoidLRCFitterLogisticSigmoidLRCFitter_predictGPPNonrectangularLRCFitterNonrectangularLRCFitter_getParameterNamesNonrectangularLRCFitter_predictGPPpartGLControlpartGLControlLasslopCompatiblepartGLExtractStandardDatapartitionNEEGLPOSIXctToBerkeleyJulianDateread_from_ameriflux22read_from_fluxnet15RectangularLRCFitterRectangularLRCFitter_predictGPPRectangularLRCFitterCVersionREddyProc_defaultunitsrenameVariablesInDataframesEddyProcsEddyProc_initializesEddyProc_sApplyUStarScensEddyProc_sCalcPotRadiationsEddyProc_sEstimateUstarScenariossEddyProc_sEstUstarTholdsEddyProc_sEstUstarThresholdsEddyProc_sEstUstarThresholdDistributionsEddyProc_sExportDatasEddyProc_sExportResultssEddyProc_sFillInitsEddyProc_sFillLUTsEddyProc_sFillMDCsEddyProc_sFillVPDFromDewsEddyProc_sGetDatasEddyProc_sGetEstimatedUstarThresholdDistributionsEddyProc_sGetUstarScenariossEddyProc_sGetUstarSuffixessEddyProc_sGLFluxPartitionsEddyProc_sGLFluxPartitionUStarScenssEddyProc_sMDSGapFillsEddyProc_sMDSGapFillAfterUstarsEddyProc_sMDSGapFillAfterUStarDistrsEddyProc_sMDSGapFillUStarScenssEddyProc_sMRFluxPartitionsEddyProc_sMRFluxPartitionUStarScenssEddyProc_sPlotDailySumssEddyProc_sPlotDailySumsYsEddyProc_sPlotDiurnalCyclesEddyProc_sPlotDiurnalCycleMsEddyProc_sPlotFingerprintsEddyProc_sPlotFingerprintYsEddyProc_sPlotHHFluxessEddyProc_sPlotHHFluxesYsEddyProc_sPlotNEEVersusUStarForSeasonsEddyProc_sSetLocationInfosEddyProc_sSetUstarScenariossEddyProc_sSetUStarSeasonssEddyProc_sTKFluxPartitionsEddyProc_sTKFluxPartitionUStarScenssEddyProc_update_ustarthreshold_columnssEddyProc_useAnnualUStarThresholdssEddyProc_useSeaonsalUStarThresholdsusControlUstarEstusControlUstarSubsettingusCreateSeasonFactorMonthusCreateSeasonFactorMonthWithinYearusCreateSeasonFactorYdayusCreateSeasonFactorYdayYearusEstUstarThresholdusEstUstarThresholdSingleFw1BinnedusEstUstarThresholdSingleFw2BinnedusGetAnnualSeasonUStarMapusGetSeasonalSeasonUStarMapusGetYearOfSeason

Dependencies:bigleafbitbit64clicliprcpp11crayonDEoptimRdplyrfansigenericsgluehmslifecyclelubridatemagrittrmlegppillarpkgconfigprettyunitsprogresspurrrR6Rcppreadrrlangrobustbasesolartimetibbletidyselecttimechangetzdbutf8vctrsvroomwithr

DEGeb example: UStar estimation

Rendered fromDEGebExample.Rmdusingknitr::knitron Nov 25 2024.

Last update: 2019-03-30
Started: 2016-01-29

different treatments of uStar threshold

Rendered fromuStarCases.Rmdusingknitr::knitron Nov 25 2024.

Last update: 2019-05-23
Started: 2018-01-08

extended use of gap-filling

Rendered fromgapFilling.Rmdusingknitr::knitron Nov 25 2024.

Last update: 2018-10-17
Started: 2018-01-08

REddyProc typical workflow

Rendered fromuseCase.Rmdusingknitr::rmarkdown_notangleon Nov 25 2024.

Last update: 2023-01-20
Started: 2018-01-08

Uncertainty aggregation

Rendered fromaggUncertainty.Rmdusingknitr::rmarkdown_notangleon Nov 25 2024.

Last update: 2022-09-02
Started: 2018-10-18

Using bigleaf functions

Rendered frombigleaf.Rmdusingknitr::rmarkdown_notangleon Nov 25 2024.

Last update: 2022-01-27
Started: 2019-03-29

Readme and manuals

Help Manual

Help pageTopics
Post Processing of (Half-)Hourly Eddy-Covariance MeasurementsREddyProc-package REddyProc
BerkeleyJulianDateToPOSIXctBerkeleyJulianDateToPOSIXct
Eddy covariance data from Gebesee crop site, GermanyDEGebExample
Estimate VPD from assuming dewpoint at daily minimum temperatureestimate_vpd_from_dew
Eddy covariance data from Tharandt, GermanyExample_DETha98
extract processing results with columns corresponding to Fluxnet15 releaseextract_FN15
fCalcAVPfromVMFandPressfCalcAVPfromVMFandPress
fCalcETfromLEfCalcETfromLE
fCalcExtRadiationfCalcExtRadiation
fCalcPotRadiationfCalcPotRadiation
fCalcRHfromAVPandTairfCalcRHfromAVPandTair
fCalcSVPfromTairfCalcSVPfromTair
fCalcVPDfromRHandTairfCalcVPDfromRHandTair
fCheckHHTimeSeriesfCheckHHTimeSeries
fConvertCtoKfConvertCtoK
fConvertGlobalToVisiblefConvertGlobalToVisible
fConvertKtoCfConvertKtoC
fConvertTimeToPosixfConvertTimeToPosix
fConvertVisibleWm2toPhotonsfConvertVisibleWm2toPhotons
filter entire daysfilter_entire_days
filter years eopfilter_years_eop
filterLongRunsfilterLongRuns
filterLongRunsInVectorfilterLongRunsInVector
fKeepColumnAttributesfKeepColumnAttributes
Temperature dependence of soil respirationfLloydTaylor
Read basic variables from Ameriflux standard (as of 2022) filesfLoadAmeriflux22
fLoadEuroFlux16fLoadEuroFlux16
Read a file in the format of Fluxnet 2015 releasefLoadFluxnet15
Load text file with one header and one unit row into data framefLoadTXTIntoDataframe
fSplitDateTimefSplitDateTime
fWriteDataframeToFilefWriteDataframeToFile
fWriteFrench23fWriteFrench23
get day boundariesget_day_boundaries
Get the timestep in fractional hoursget_timestep_hours
getAmerifluxToBGC05VariableNameMappinggetAmerifluxToBGC05VariableNameMapping
getBGC05ToAmerifluxVariableNameMappinggetBGC05ToAmerifluxVariableNameMapping
getExamplePathgetExamplePath
getFilledExampleDETha98DatagetFilledExampleDETha98Data
getREddyProcExampleDirgetREddyProcExampleDir
getTZonegetTZone
globalDummyVarssDATA sID sINFO sLOCATION sTEMP sUSTAR
help DateTimeshelp_DateTimes
help exporthelp_export
LightResponseCurveFitterLightResponseCurveFitter
LightResponseCurveFitter computeCostLightResponseCurveFitter_computeCost
LightResponseCurveFitter computeLRCGradientLightResponseCurveFitter_computeLRCGradient
LightResponseCurveFitter fitLRCLightResponseCurveFitter_fitLRC
LightResponseCurveFitter getOptimizedParameterPositionsLightResponseCurveFitter_getOptimizedParameterPositions
LightResponseCurveFitter getParameterInitialsLightResponseCurveFitter_getParameterInitials
LightResponseCurveFitter getParameterNamesLightResponseCurveFitter_getParameterNames
LightResponseCurveFitter getPriorLocationLightResponseCurveFitter_getPriorLocation
LightResponseCurveFitter getPriorScaleLightResponseCurveFitter_getPriorScale
LightResponseCurveFitter isParameterInBoundsLightResponseCurveFitter_isParameterInBounds
LightResponseCurveFitter optimLRCLightResponseCurveFitter_optimLRC
LightResponseCurveFitter optimLRCBoundsLightResponseCurveFitter_optimLRCBounds
LightResponseCurveFitter optimLRCOnAdjustedPriorLightResponseCurveFitter_optimLRCOnAdjustedPrior
LightResponseCurveFitter predictGPPLightResponseCurveFitter_predictGPP
LightResponseCurveFitter predictLRCLightResponseCurveFitter_predictLRC
Class '"LightResponseCurveFitter"'LightResponseCurveFitter-class
LogisticSigmoidLRCFitterLogisticSigmoidLRCFitter
LogisticSigmoidLRCFitter predictGPPLogisticSigmoidLRCFitter_predictGPP
Class '"LogisticSigmoidLRCFitter"'LogisticSigmoidLRCFitter-class
NonrectangularLRCFitterNonrectangularLRCFitter
NonrectangularLRCFitter getParameterNamesNonrectangularLRCFitter_getParameterNames
NonrectangularLRCFitter predictGPPNonrectangularLRCFitter_predictGPP
Class '"NonrectangularLRCFitter"'NonrectangularLRCFitter-class
partGLControlpartGLControl
partGLControlLasslopCompatiblepartGLControlLasslopCompatible
partGLExtractStandardDatapartGLExtractStandardData
partitionNEEGLpartitionNEEGL
POSIXctToBerkeleyJulianDatePOSIXctToBerkeleyJulianDate
Extract basic variables from Ameriflux standard (as of 2022) data.framesread_from_ameriflux22
extract REddyProc input columns from data.frame in Fluxnet15 formatread_from_fluxnet15
RectangularLRCFitterRectangularLRCFitter
RectangularLRCFitter predictGPPRectangularLRCFitter_predictGPP
Class '"RectangularLRCFitter"'RectangularLRCFitter-class
RectangularLRCFitterCVersionRectangularLRCFitterCVersion
Class '"RectangularLRCFitterCVersion"'RectangularLRCFitterCVersion-class
Get the default units for given variablesREddyProc_defaultunits
renameVariablesInDataframerenameVariablesInDataframe
RHLightResponseCostCRHLightResponseCostC _REddyProc_RHLightResponseCostC
sEddyProcsEddyProc
sEddyProc initializesEddyProc_initialize
sEddyProc sApplyUStarScensEddyProc_sApplyUStarScen
sEddyProc sCalcPotRadiationsEddyProc_sCalcPotRadiation
sEddyProc sEstimateUstarScenariossEddyProc_sEstimateUstarScenarios
sEddyProc$sEstUstarThreshold - Estimating ustar thresholdsEddyProc_sEstUstarThold
sEddyProc$sEstUstarThreshold - Estimating ustar thresholdsEddyProc_sEstUstarThreshold
sEddyProc sEstUstarThresholdDistributionsEddyProc_sEstUstarThresholdDistribution
sEddyProc sExportDatasEddyProc_sExportData
sEddyProc sExportResultssEddyProc_sExportResults
sEddyProc$sFillInit - Initialize gap fillingsEddyProc_sFillInit
sEddyProc sFillLUTsEddyProc_sFillLUT
sEddyProc sFillMDCsEddyProc_sFillMDC
Estimate VPD from daily minimum temperaturesEddyProc_sFillVPDFromDew
sEddyProc sGetDatasEddyProc_sGetData
sEddyProc sGetEstimatedUstarThresholdDistributionsEddyProc_sGetEstimatedUstarThresholdDistribution
sEddyProc sGetUstarScenariossEddyProc_sGetUstarScenarios
sEddyProc sGetUstarSuffixessEddyProc_sGetUstarSuffixes
sEddyProc sGLFluxPartitionsEddyProc_sGLFluxPartition
sEddyProc sGLFluxPartitionUStarScenssEddyProc_sGLFluxPartitionUStarScens
sEddyProc sMDSGapFillsEddyProc_sMDSGapFill
sEddyProc sMDSGapFillAfterUstarsEddyProc_sMDSGapFillAfterUstar
sEddyProc sMDSGapFillAfterUStarDistrsEddyProc_sMDSGapFillAfterUStarDistr
sEddyProc sMDSGapFillUStarScenssEddyProc_sMDSGapFillUStarScens
sEddyProc sMRFluxPartitionsEddyProc_sMRFluxPartition
sEddyProc sMRFluxPartitionUStarScenssEddyProc_sMRFluxPartitionUStarScens
sEddyProc$sPlotDailySums - Image with daily sums of each yearsEddyProc_sPlotDailySums
sEddyProc sPlotDailySumsYsEddyProc_sPlotDailySumsY
sEddyProc sPlotDiurnalCyclesEddyProc_sPlotDiurnalCycle
sEddyProc sPlotDiurnalCycleMsEddyProc_sPlotDiurnalCycleM
sEddyProc sPlotFingerprintsEddyProc_sPlotFingerprint sPlotFingerprint
sEddyProc sPlotFingerprintYsEddyProc_sPlotFingerprintY
sEddyProc sPlotHHFluxessEddyProc_sPlotHHFluxes
sEddyProc sPlotHHFluxesYsEddyProc_sPlotHHFluxesY
sEddyProc sPlotNEEVersusUStarForSeasonsEddyProc_sPlotNEEVersusUStarForSeason
sEddyProc sSetLocationInfosEddyProc_sSetLocationInfo
sEddyProc sSetUstarScenariossEddyProc_sSetUstarScenarios
sEddyProc sSetUStarSeasonssEddyProc_sSetUStarSeasons
sEddyProc sTKFluxPartitionsEddyProc_sTKFluxPartition
sEddyProc sTKFluxPartitionUStarScenssEddyProc_sTKFluxPartitionUStarScens
Add columns reporting the uStar threshold for each scenario to sDATAsEddyProc_update_ustarthreshold_columns
sEddyProc useAnnualUStarThresholdssEddyProc_useAnnualUStarThresholds
sEddyProc useSeaonsalUStarThresholdssEddyProc_useSeaonsalUStarThresholds
Class '"sEddyProc"'sEddyProc-class
usControlUstarEstusControlUstarEst
usControlUstarSubsettingusControlUstarSubsetting
usCreateSeasonFactorMonthusCreateSeasonFactorMonth
usCreateSeasonFactorMonthWithinYearusCreateSeasonFactorMonthWithinYear
usCreateSeasonFactorYdayusCreateSeasonFactorYday
usCreateSeasonFactorYdayYearusCreateSeasonFactorYdayYear
usEstUstarThreshold - Estimating ustar thresholdusEstUstarThreshold
usEstUstarThresholdSingleFw1BinnedusEstUstarThresholdSingleFw1Binned
usEstUstarThresholdSingleFw2BinnedusEstUstarThresholdSingleFw2Binned
usGetAnnualSeasonUStarMapusGetAnnualSeasonUStarMap
usGetSeasonalSeasonUStarMapusGetSeasonalSeasonUStarMap
usGetYearOfSeasonusGetYearOfSeason