partGLExtractStandardData: partGLExtractStandardData

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

partGLExtractStandardData

Description

Relevant columns from original input with defined names

Usage

partGLExtractStandardData(ds, NEEVar = paste0("NEE", 
    suffixDash, "_f"), QFNEEVar = if (!missing(QFNEEVar.s)) QFNEEVar.s else paste0("NEE", 
    suffixDash, "_fqc"), QFNEEValue = if (!missing(QFNEEValue.n)) QFNEEValue.n else 0, 
    NEESdVar = if (!missing(NEESdVar.s)) NEESdVar.s else paste0("NEE", 
        suffixDash, "_fsd"), TempVar = paste0("Tair_f"), 
    QFTempVar = if (!missing(QFTempVar.s)) QFTempVar.s else paste0("Tair_fqc"), 
    QFTempValue = if (!missing(QFTempValue.n)) QFTempValue.n else 0, 
    VPDVar = if (!missing(VPDVar.s)) VPDVar.s else paste0("VPD_f"), 
    QFVPDVar = if (!missing(QFVPDVar.s)) QFVPDVar.s else paste0("VPD_fqc"), 
    QFVPDValue = if (!missing(QFVPDValue.n)) QFVPDValue.n else 0, 
    RadVar = if (!missing(RadVar.s)) RadVar.s else "Rg_f", 
    QFRadVar = if (!missing(QFRadVar.s)) QFRadVar.s else paste0("Rg_fqc"), 
    QFRadValue = if (!missing(QFRadValue.n)) QFRadValue.n else 0, 
    PotRadVar = if (!missing(PotRadVar.s)) PotRadVar.s else "PotRad_NEW", 
    suffix = if (!missing(Suffix.s)) Suffix.s else "", 
    NEEVar.s, QFNEEVar.s, QFNEEValue.n, NEESdVar.s, 
    TempVar.s, QFTempVar.s, QFTempValue.n, 
    VPDVar.s, QFVPDVar.s, QFVPDValue.n, RadVar.s, 
    QFRadVar.s, QFRadValue.n, PotRadVar.s, 
    Suffix.s, controlGLPart = partGLControl())

Arguments

ds	dataset with all the specified input columns and full days in equidistant times
NEEVar	Variable of NEE
QFNEEVar	Quality flag of variable
QFNEEValue	Value of quality flag for _good_ (original) data
NEESdVar	Variable of standard deviation of net ecosystem fluxes
TempVar	Filled air or soil temperature variable (degC)
QFTempVar	Quality flag of filled temperature variable
QFTempValue	Value of temperature quality flag for _good_ (original) data
VPDVar	Filled Vapor Pressure Deficit, VPD (hPa)
QFVPDVar	Quality flag of filled VPD variable
QFVPDValue	Value of VPD quality flag for _good_ (original) data
RadVar	Filled radiation variable
QFRadVar	Quality flag of filled radiation variable
QFRadValue	Value of radiation quality flag for _good_ (original) data
PotRadVar	Variable name of potential rad. (W / m2)
suffix	string inserted into column names before identifier for NEE column defaults (see sEddyProc_sMDSGapFillAfterUstar).
NEEVar.s	deprecated
QFNEEVar.s	deprecated
QFNEEValue.n	deprecated
NEESdVar.s	deprecated
TempVar.s	deprecated
QFTempVar.s	deprecated
QFTempValue.n	deprecated
VPDVar.s	deprecated
QFVPDVar.s	deprecated
QFVPDValue.n	deprecated
RadVar.s	deprecated
QFRadVar.s	deprecated
QFRadValue.n	deprecated
PotRadVar.s	deprecated
Suffix.s	deprecated
controlGLPart	further default parameters, see partGLControl

Details

The LRC fit usually weights NEE records by its uncertainty. In order to also use records with missing NEESdVar, uncertainty of the missing values is by default set to a conservatively high value, parameterized by controlGLPart$replaceMissingSdNEEParms). Controlled by argument replaceMissingSdNEEParms in partGLControl, but overruled by argument neglectNEEUncertaintyOnMissing.

Value

a data.frame with columns

sDateTime	first column of ds, usually the time stamp not used, but usually first column is a DateTime is kept for aiding debug
NEE	NEE filtered for quality flay
sdNEE	standard deviation of NEE with missing values replaced
Temp	Temperature, quality filtered if isTRUE(controlGLPart$isFilterMeteoQualityFlag)
VPD	Water pressure deficit, quality filtered if isTRUE(controlGLPart$isFilterMeteoQualityFlag)
Rg	Incoming radiation
isDay	Flag that is true for daytime records
isNight	Flag that is true for nighttime records

Author(s)

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

bgctw/REddyProc documentation built on March 26, 2024, 11:35 p.m.