partGLControl: partGLControl

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

partGLControl

Description

Default list of parameters for Lasslop 2010 daytime flux partitioning For highest compatibility to the pvWave code of G.Lasslop (used by first BGC-online tool) see function partGLControlLasslopCompatible.

Usage

partGLControl(LRCFitConvergenceTolerance = 0.001, 
    nLRCFitConvergenceTolerance = 0.001, 
    nBootUncertainty = 30L, minNRecInDayWindow = 10L, 
    isAssociateParmsToMeanOfValids = TRUE, 
    isLasslopPriorsApplied = TRUE, isUsingLasslopQualityConstraints = FALSE, 
    isSdPredComputed = TRUE, isFilterMeteoQualityFlag = FALSE, 
    isBoundLowerNEEUncertainty = TRUE, fixedTRefAtNightTime = NA, 
    isExtendTRefWindow = TRUE, smoothTempSensEstimateAcrossTime = TRUE, 
    isNeglectPotRadForNight = FALSE, NRHRfunction = FALSE, 
    isNeglectVPDEffect = FALSE, isRefitMissingVPDWithNeglectVPDEffect = TRUE, 
    fixedTempSens = data.frame(E0 = NA_real_, 
        sdE0 = NA_real_, RRef = NA_real_), 
    replaceMissingSdNEEParms = c(perc = 0.2, 
        minSd = 0.7), neglectNEEUncertaintyOnMissing = FALSE, 
    minPropSaturation = NA, useNightimeBasalRespiration = FALSE)

Arguments

LRCFitConvergenceTolerance	convergence criterion for rectangular light response curve fit. If relative improvement of reducing residual sum of squares between predictions and observations is less than this criterion, assume convergence. Decrease to get more precise parameter estimates, Increase for speedup.
nLRCFitConvergenceTolerance	convergence criterion for nonrectangular light response curve fit. Here its a factor of machine tolerance.
nBootUncertainty	number of bootstrap samples for estimating uncertainty. Set to zero to derive uncertainty from curvature of a single fit
minNRecInDayWindow	Minimum number of data points for regression
isAssociateParmsToMeanOfValids	set to FALSE to associate parameters to the first record of the window for interpolation instead of mean across valid records inside a window
isLasslopPriorsApplied	set to TRUE to apply strong fixed priors on LRC fitting. Returned parameter estimates claimed valid for some case where not enough data was available
isUsingLasslopQualityConstraints	set to TRUE to avoid quality constraints additional to Lasslop 2010
isSdPredComputed	set to FALSE to avoid computing standard errors of Reco and GPP for small performance increase
isFilterMeteoQualityFlag	set to TRUE to use only records where quality flag of meteo drivers (radiation, temperature, VPD) is zero, i.e. non-gapfilled for parameter estimation. For prediction, the gap-filled value is used always, to produce predictions also for gaps.
isBoundLowerNEEUncertainty	set to FALSE to avoid adjustment of very low uncertainties before day-Time fitting that avoids the high leverage those records with unreasonable low uncertainty.
fixedTRefAtNightTime	if a finite value (degree Centigrade) is given, it is used instead of median data temperature as reference temperature in estimation of temperature sensitivity from night data
isExtendTRefWindow	set to FALSE to avoid successively extending the night-time window in order to estimate a temperature sensitivity where previous estimates failed
smoothTempSensEstimateAcrossTime	set to FALSE to use independent estimates of temperature sensitivity on each windows instead of a vector of E0 that is smoothed over time
isNeglectPotRadForNight	set to TRUE to not use potential radiation in determining night-time data.
NRHRfunction	deprecated: Flag if TRUE use the NRHRF for partitioning; Now use lrcFitter = NonrectangularLRCFitter()
isNeglectVPDEffect	set to TRUE to avoid using VPD in the computations. This may help when VPD is rarely measured.
isRefitMissingVPDWithNeglectVPDEffect	set to FALSE to avoid repeating estimation with isNeglectVPDEffect = TRUE trying to predict when VPD is missing
fixedTempSens	data.frame of one row or nRow = nWindow corresponding to return value of partGLFitNightTimeTRespSens While column RRef is used only as a prior and initial value for the daytime-fitting and can be NA, E0 is used as given temperature sensitivity and varied according to sdE0 in the bootstrap.
replaceMissingSdNEEParms	parameters for replacing missing standard deviation of NEE. see replaceMissingSdByPercentage. Default sets missing uncertainty to 20% of NEE but at least 0.7 flux-units (usually mumol CO2 / m2 / s). Specify c(NA, NA) to avoid replacing missings in standard deviation of NEE and to omit those records from LRC fit.
neglectNEEUncertaintyOnMissing	If set to TRUE: if there are records with missing uncertainty of NEE inside one window, set all uncertainties to 1. This overrules option replaceMissingSdNEEParms.
minPropSaturation	quality criterion for sufficient data in window. If GPP prediction of highest PAR of window is less than minPropSaturation * (GPP at light-saturation, i.e. beta) this indicates that PAR is not sufficiently high to constrain the shape of the LRC
useNightimeBasalRespiration	set to TRUE to estimate nighttime respiration based on basal respiration estimated on nighttime data instead of basal respiration estimated from daytime data. This implements the modified daytime method from Keenan 2019 (doi:10.1038/s41559-019-0809-2)

Value

list with entries of given arguments.

Author(s)

TW 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]

See Also

partitionNEEGL

Examples

partGLControl(nBootUncertainty = 40L)

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