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

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

Author(Department for Biogeochemical Integration at MPI-BGC, Jena, Germany)
Date of publication2016-08-31 13:31:19
MaintainerDepartment for Biogeochemical Integration <REddyProc-help@bgc.mpg.de>
LicenseGPL (>= 2)
Version0.8-2
http://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb, http://r-forge.r-project.org/projects/reddyproc/

View on R-Forge

Man pages

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

fFullYearTimeSteps: fFullYearTimeSteps

fGetBeginOfEddyPeriod: fGetBeginOfEddyPeriod

fGetEndOfEddyPeriod: fGetEndOfEddyPeriod

fGetYearOfEddyPeriod: fGetYearOfEddyPeriod

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

POSIXctToBerkeleyJulianDate: POSIXctToBerkeleyJulianDate

REddyProc-package: Data processing and plotting utilities of (half-)hourly...

renameVariablesInDataframe: renameVariablesInDataframe

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

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...

usControlUstarEst: usControlUstarEst

usControlUstarSubsetting: usControlUstarSubsetting

usCreateSeasonFactorMonth: usCreateSeasonFactorMonth

usCreateSeasonFactorMonthWithinYear: usCreateSeasonFactorMonthWithinYear

usCreateSeasonFactorYday: usCreateSeasonFactorYday

usCreateSeasonFactorYdayYear: usCreateSeasonFactorYdayYear

usEstUstarThreshold: sEddyProc$sEstUstarThreshold - Estimating ustar threshold

usEstUstarThresholdSingleFw1Binned: usEstUstarThresholdSingleFw1Binned

usEstUstarThresholdSingleFw2Binned: usEstUstarThresholdSingleFw2Binned

usGetAnnualSeasonUStarMappingFromDistributionResult: usGetAnnualSeasonUStarMappingFromDistributionResult

usGetSeaonalSeasonUStarMappingFromDistributionResult: usGetSeaonalSeasonUStarMappingFromDistributionResult

usGetValidUstarIndices: usGetValidUstarIndices

usGetYearOfSeason: usGetYearOfSeason

Functions

BerkeleyJulianDateToPOSIXct Man page
DEGebExample Man page
Example_DETha98 Man page
fAddNCFVar Man page
fCalcAVPfromVMFandPress Man page
fCalcETfromLE Man page
fCalcExtRadiation Man page
fCalcLengthOfGaps Man page
fCalcPotRadiation Man page
fCalcRHfromAVPandTair Man page
fCalcSunPosition Man page
fCalcSVPfromTair Man page
fCalcVPDfromRHandTair Man page
fCheckColNames Man page
fCheckColNum Man page
fCheckColPlausibility Man page
fCheckHHTimeSeries Man page
fCheckOutsideRange Man page
fCheckValNum Man page
fCheckValString Man page
fConvertCtoK Man page
fConvertGapsToNA Man page
fConvertGlobalToVisible Man page
fConvertKtoC Man page
fConvertNAsToGap Man page
fConvertTimeToPosix Man page
fConvertVisibleWm2toPhotons Man page
fExpandToFullYear Man page
fFullYearTimeSteps Man page
fGetBeginOfEddyPeriod Man page
fGetEndOfEddyPeriod Man page
fGetYearOfEddyPeriod Man page
fInitFilesDir Man page
fInterpolateGaps Man page
fLloydTaylor Man page
fLoadEuroFlux16 Man page
fLoadFluxNCInfo Man page
fLoadFluxNCIntoDataframe Man page
fLoadTXTIntoDataframe Man page
fOptimSingleE0 Man page
fOptimSingleE0_Lev Man page
fReadTimeBerkeley Man page
fReadTimeSeveralCols Man page
fRegrE0fromShortTerm Man page
fSetFile Man page
fSetQF Man page
fStripFileExtension Man page
fWriteDataframeToFile Man page
getAmerifluxToBGC05VariableNameMapping Man page
getBGC05ToAmerifluxVariableNameMapping Man page
POSIXctToBerkeleyJulianDate Man page
REddyProc Man page
REddyProc-package Man page
renameVariablesInDataframe Man page
sEddyProc.example Man page
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
sGetData Man page
sMDSGapFill Man page
sMDSGapFillAfterUstar Man page
sMDSGapFillAfterUStarDistr 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
usControlUstarEst Man page
usControlUstarSubsetting Man page
usCreateSeasonFactorMonth Man page
usCreateSeasonFactorMonthWithinYear Man page
usCreateSeasonFactorYday Man page
usCreateSeasonFactorYdayYear Man page
usEstUstarThreshold Man page
usEstUstarThresholdSingleFw1Binned Man page
usEstUstarThresholdSingleFw2Binned Man page
usGetAnnualSeasonUStarMappingFromDistributionResult Man page
usGetSeaonalSeasonUStarMappingFromDistributionResult Man page
usGetValidUstarIndices Man page
usGetYearOfSeason Man page

Files

REddyProc/DESCRIPTION
REddyProc/NAMESPACE
REddyProc/R
REddyProc/R/DataFunctions.R REddyProc/R/Eddy.R REddyProc/R/EddyGapfilling.R REddyProc/R/EddyPartitioning.R REddyProc/R/EddyPlotting.R REddyProc/R/EddyUStarFilterChangePointDetection.R REddyProc/R/EddyUStarFilterDP.R REddyProc/R/Example.R REddyProc/R/FileHandling.R REddyProc/R/FileHandlingFormats.R REddyProc/R/GeoFunctions.R REddyProc/R/RcppExports.R REddyProc/R/cFunc.R REddyProc/R/variableNames.R REddyProc/R/zzzDebugCode.R
REddyProc/build
REddyProc/build/vignette.rds
REddyProc/data
REddyProc/data/DEGebExample.RData
REddyProc/data/Example_DETha98.RData
REddyProc/data/datalist
REddyProc/inst
REddyProc/inst/develop
REddyProc/inst/develop/DevelopmentNotes.docx
REddyProc/inst/develop/FlowDiagramGapfilling.pptx
REddyProc/inst/develop/MDSFlow.jpg
REddyProc/inst/develop/OutputColsExample.xlsx
REddyProc/inst/develop/compOldNewTool.R
REddyProc/inst/develop/genDEGebExample.R
REddyProc/inst/develop/genDocu
REddyProc/inst/develop/genDocu/DEGebExample.Rd REddyProc/inst/develop/genDocu/Example_DETha98.Rd REddyProc/inst/develop/genDocu/REddyProc-package.Rd
REddyProc/inst/develop/genOldToolData.R
REddyProc/inst/develop/genRpackage.R
REddyProc/inst/develop/setREnvir.R
REddyProc/inst/develop/templateInlinedocs.R
REddyProc/inst/develop/testEddyProc.R
REddyProc/inst/doc
REddyProc/inst/doc/DEGebExample.Rmd
REddyProc/inst/doc/DEGebExample.html
REddyProc/inst/examples
REddyProc/inst/examples/Example_DE-Tha.1996.1998.hourly.nc
REddyProc/inst/examples/Example_DETha98.txt
REddyProc/inst/examples/Example_DETha98_PVWave_DataSetafterFluxpart.txt
REddyProc/inst/examples/PVWave_TH98_new.txt
REddyProc/inst/scripts
REddyProc/inst/scripts/DataFunctions.R
REddyProc/inst/scripts/Eddy.R
REddyProc/inst/scripts/EddyGapfilling.R
REddyProc/inst/scripts/EddyPartitioning.R
REddyProc/inst/scripts/EddyPlotting.R
REddyProc/inst/scripts/EddyUStarFilterChangePointDetection.R
REddyProc/inst/scripts/EddyUStarFilterDP.R
REddyProc/inst/scripts/FileHandling.R
REddyProc/inst/scripts/GeoFunctions.R
REddyProc/inst/scripts/RcppExports.R
REddyProc/inst/scripts/cFunc.R
REddyProc/inst/scripts/zzzDebugCode.R
REddyProc/inst/tests
REddyProc/inst/tests/test_UStarFilter.R
REddyProc/inst/tests/test_binWithEqualValues.R
REddyProc/inst/tests/test_fCalcPotRadiation.R
REddyProc/inst/tests/test_fCheckValue.R
REddyProc/inst/tests/test_fConvertTimeToPosix.R
REddyProc/inst/tests/test_sEddyProc.R
REddyProc/inst/tests/test_sEddyProc_Partitioning.R
REddyProc/inst/tests2
REddyProc/inst/tests2/test_readNcdf.R
REddyProc/man
REddyProc/man/BerkeleyJulianDateToPOSIXct.Rd REddyProc/man/DEGebExample.Rd REddyProc/man/Example_DETha98.Rd REddyProc/man/POSIXctToBerkeleyJulianDate.Rd REddyProc/man/REddyProc-package.Rd REddyProc/man/fAddNCFVar.Rd REddyProc/man/fCalcAVPfromVMFandPress.Rd REddyProc/man/fCalcETfromLE.Rd REddyProc/man/fCalcExtRadiation.Rd REddyProc/man/fCalcLengthOfGaps.Rd REddyProc/man/fCalcPotRadiation.Rd REddyProc/man/fCalcRHfromAVPandTair.Rd REddyProc/man/fCalcSVPfromTair.Rd REddyProc/man/fCalcSunPosition.Rd REddyProc/man/fCalcVPDfromRHandTair.Rd REddyProc/man/fCheckColNames.Rd REddyProc/man/fCheckColNum.Rd REddyProc/man/fCheckColPlausibility.Rd REddyProc/man/fCheckHHTimeSeries.Rd REddyProc/man/fCheckOutsideRange.Rd REddyProc/man/fCheckValNum.Rd REddyProc/man/fCheckValString.Rd REddyProc/man/fConvertCtoK.Rd REddyProc/man/fConvertGapsToNA.Rd REddyProc/man/fConvertGlobalToVisible.Rd REddyProc/man/fConvertKtoC.Rd REddyProc/man/fConvertNAsToGap.Rd REddyProc/man/fConvertTimeToPosix.Rd REddyProc/man/fConvertVisibleWm2toPhotons.Rd REddyProc/man/fExpandToFullYear.Rd REddyProc/man/fFullYearTimeSteps.Rd REddyProc/man/fGetBeginOfEddyPeriod.Rd REddyProc/man/fGetEndOfEddyPeriod.Rd REddyProc/man/fGetYearOfEddyPeriod.Rd REddyProc/man/fInitFilesDir.Rd REddyProc/man/fInterpolateGaps.Rd REddyProc/man/fLloydTaylor.Rd REddyProc/man/fLoadEuroFlux16.Rd REddyProc/man/fLoadFluxNCInfo.Rd REddyProc/man/fLoadFluxNCIntoDataframe.Rd REddyProc/man/fLoadTXTIntoDataframe.Rd REddyProc/man/fOptimSingleE0.Rd REddyProc/man/fOptimSingleE0_Lev.Rd REddyProc/man/fReadTimeBerkeley.Rd REddyProc/man/fReadTimeSeveralCols.Rd REddyProc/man/fRegrE0fromShortTerm.Rd REddyProc/man/fSetFile.Rd REddyProc/man/fSetQF.Rd REddyProc/man/fStripFileExtension.Rd REddyProc/man/fWriteDataframeToFile.Rd REddyProc/man/getAmerifluxToBGC05VariableNameMapping.Rd REddyProc/man/getBGC05ToAmerifluxVariableNameMapping.Rd REddyProc/man/renameVariablesInDataframe.Rd REddyProc/man/sEddyProc.example.Rd REddyProc/man/sEddyProc.new.Rd REddyProc/man/sEstUstarThreshold.Rd REddyProc/man/sEstUstarThresholdDistribution.Rd REddyProc/man/sExportData.Rd REddyProc/man/sExportResults.Rd REddyProc/man/sFillInit.Rd REddyProc/man/sFillLUT.Rd REddyProc/man/sFillMDC.Rd REddyProc/man/sGetData.Rd REddyProc/man/sMDSGapFill.Rd REddyProc/man/sMDSGapFillAfterUStarDistr.Rd REddyProc/man/sMDSGapFillAfterUstar.Rd REddyProc/man/sMRFluxPartition.Rd REddyProc/man/sPlotDailySums.Rd REddyProc/man/sPlotDailySumsY.Rd REddyProc/man/sPlotDiurnalCycle.Rd REddyProc/man/sPlotFingerprint.Rd REddyProc/man/sPlotFingerprintY.Rd REddyProc/man/sPlotHHFluxes.Rd REddyProc/man/sPlotHHFluxesY.Rd REddyProc/man/sPlotNEEVersusUStarForSeason.Rd REddyProc/man/sPrintFrames.Rd REddyProc/man/sRegrE0fromShortTerm.Rd REddyProc/man/sRegrRref.Rd REddyProc/man/usControlUstarEst.Rd REddyProc/man/usControlUstarSubsetting.Rd REddyProc/man/usCreateSeasonFactorMonth.Rd REddyProc/man/usCreateSeasonFactorMonthWithinYear.Rd REddyProc/man/usCreateSeasonFactorYday.Rd REddyProc/man/usCreateSeasonFactorYdayYear.Rd REddyProc/man/usEstUstarThreshold.Rd REddyProc/man/usEstUstarThresholdSingleFw1Binned.Rd REddyProc/man/usEstUstarThresholdSingleFw2Binned.Rd REddyProc/man/usGetAnnualSeasonUStarMappingFromDistributionResult.Rd REddyProc/man/usGetSeaonalSeasonUStarMappingFromDistributionResult.Rd REddyProc/man/usGetValidUstarIndices.Rd REddyProc/man/usGetYearOfSeason.Rd
REddyProc/src
REddyProc/src/RcppExports.cpp
REddyProc/src/whichValueGreaterEqualC.cpp
REddyProc/tests
REddyProc/tests/doRUnit.R
REddyProc/vignettes
REddyProc/vignettes/DEGebExample.Rmd

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