Different treatments of uStar threshold

The recommended way of dealing with the uncertain uStar threshold for filtering the half-hourly data, is to repeat all the processing steps with several bootstrapped estimates of the threshold as in vignette('useCase').

First, some setup.

#+++ load libraries used in this vignette
library(REddyProc)
library(dplyr)
#+++ define directory for outputs
outDir <- tempdir()  # CRAN policy dictates to write only to this dir in examples
#outDir <- "out"     # to write to subdirectory of current users dir
#+++ Add time stamp in POSIX time format to example data
EddyDataWithPosix.F <- fConvertTimeToPosix(Example_DETha98, 'YDH',Year.s = 'Year' 
    ,Day.s = 'DoY',Hour.s = 'Hour')

Not applying uStar filtering

Subsequent processing steps can be performed without further uStar filtering using sEddyProc_sMDSGapFill. Corresponding result columns then have no uStar specific suffix.

EddyProc.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, 
    c('NEE','Rg','Tair','VPD', 'Ustar'))
EddyProc.C$sMDSGapFill('NEE')
grep("NEE.*_f$",names(EddyProc.C$sExportResults()), value = TRUE)

## [1] "NEE_f"

User-specified uStar threshold

The user can provide value for uStar-filtering before gapfilling, using sEddyProc_sMDSGapFillAfterUstar. Output columns for this uStar scenario use the suffix as specified by argument UstarSuffix.s which defaults to “WithUstar”.

The friction velocity, uStar, needs to be in column named “uStar” of the input dataset.

EddyProc.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, 
    c('NEE','Rg','Tair','VPD', 'Ustar'))
uStar <- 0.46
EddyProc.C$sMDSGapFillAfterUstar('NEE', UstarThres.df = uStar)
grep("NEE.*_f$",names(EddyProc.C$sExportResults()), value = TRUE)

## [1] "NEE_WithUstar_f"

Sinlge uStar threshold estimate

The uStar threshold can be estimated from the uStar-NEE relationship from the data without its uncertainty by bootstrap.

EddyProc.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, 
    c('NEE','Rg','Tair','VPD', 'Ustar'))
# estimating the thresholds based on the data (without bootstrap)
(uStarTh <- EddyProc.C$sEstUstarThreshold()$uStarTh)

##   aggregationMode seasonYear  season     uStar
## 1          single         NA    <NA> 0.4162500
## 2            year       1998    <NA> 0.4162500
## 3          season       1998 1998001 0.4162500
## 4          season       1998 1998003 0.4162500
## 5          season       1998 1998006 0.3520000
## 6          season       1998 1998009 0.3369231
## 7          season       1998 1998012 0.1740000

# may plot saturation of NEE with UStar for a specified season to pdf
EddyProc.C$sPlotNEEVersusUStarForSeason(levels(uStarTh$season)[3], dir = outDir )

Next, the annual estimate is used as the default in gap-filling. Output columns use the suffix as specified by argument UstarSuffix.s which defaults to “WithUstar”.

EddyProc.C$sMDSGapFillAfterUstar('NEE')
grep("NEE.*_f$",names(EddyProc.C$sExportResults()), value = TRUE)

## [1] "NEE_WithUstar_f"

See also

A more advanced case of user-specified seasons for uStar threshold estimate is given in vignette('DEGebExample').