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

# do not execute on CRAN: 
# https://stackoverflow.com/questions/28961431/computationally-heavy-r-vignettes
is_check <- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_",
             "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
knitr::opts_chunk$set(eval = !is_check)

library(knitr)
#rmarkdown::render("vignettes/uStarCases.Rmd","md_document")
opts_knit$set(root.dir = '..')
opts_chunk$set(
    #, fig.align = "center"
    #, fig.width = 3.27, fig.height = 2.5, dev.args = list(pointsize = 10)
    #,cache = TRUE
    #, fig.width = 4.3, fig.height = 3.2, dev.args = list(pointsize = 10)
    #, fig.width = 6.3, fig.height = 6.2, dev.args = list(pointsize = 10)
    # works with html but causes problems with latex
    #,out.extra = 'style = "display:block; margin: auto"' 
    )
knit_hooks$set(spar = function(before, options, envir) {
    if (before) {
        par(las = 1 )                   #also y axis labels horizontal
        par(mar = c(2.0,3.3,0,0) + 0.3 )  #margins
        par(tck = 0.02 )                          #axe-tick length inside plots             
        par(mgp = c(1.1,0.2,0) )  #positioning of axis title, axis labels, axis
     }
})

#themeTw <- theme_bw(base_size = 10) + theme(axis.title = element_text(size = 9))

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 
# and filter long runs of equal NEE values
EddyDataWithPosix <- fConvertTimeToPosix(
  filterLongRuns(Example_DETha98, "NEE")
  , 'YDH', Year = 'Year', Day = 'DoY', Hour = '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.

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

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 which defaults to "uStar".

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

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

Single uStar threshold estimate

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

EProc <- sEddyProc$new(
  'DE-Tha', EddyDataWithPosix, c('NEE','Rg','Tair','VPD', 'Ustar'))
# estimating the thresholds based on the data (without bootstrap)
(uStarTh <- EProc$sEstUstarThold())
# may plot saturation of NEE with UStar for a specified season to pdf
EProc$sPlotNEEVersusUStarForSeason(levels(uStarTh$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 uSstarSuffix which defaults to "uStar".

#EProc$useAnnualUStarThresholds()
EProc$sMDSGapFillAfterUstar('NEE')
grep("NEE.*_f$",names(EProc$sExportResults()), value = TRUE)

Scenarios across distribution of u* threshold estimate

Choosing a different u threshold effects filtering and the subsequent processing steps of gap-filling, and flux-partitioning. In order to quantify the uncertainty due to not exactly knowing the u threshold, these processing steps should be repeated for different threshold scenarios, and the spread across the results should be investigated.

First, the quantiles of the threshold distribution are estimated by bootstrap.

EProc <- sEddyProc$new(
  'DE-Tha', EddyDataWithPosix, c('NEE','Rg','Tair','VPD', 'Ustar'))
EProc$sEstimateUstarScenarios(
    nSample = 100L, probs = c(0.05, 0.5, 0.95))
# inspect the thresholds to be used by default
EProc$sGetUstarScenarios()

By default the annually aggregated threshold estimates are used for each season within one year as in the original method publication. To see the estimates for different aggregation levels, use method sEddyProc_sGetEstimatedUstarThresholdDistribution:

(uStarThAgg <- EProc$sGetEstimatedUstarThresholdDistribution())

In conjunction with method usGetSeasonalSeasonUStarMap and sEddyProc_sSetUstarScenarios this can be used to set seasonally different u* threshold. However, this common case supported by method sEddyProc_useSeaonsalUStarThresholds.

#EProc$sSetUstarScenarios(
#  usGetSeasonalSeasonUStarMap(uStarThAgg)[,-2])
EProc$useSeaonsalUStarThresholds()
# inspect the changed thresholds to be used
EProc$sGetUstarScenarios()

Several function whose name ends with 'UstarScens' perform the subsequent processing steps for all uStar scenarios. They operate and create columns that differ between threshold scenarios by a suffix.

EProc$sMDSGapFillUStarScens("NEE")
grep("NEE_.*_f$",names(EProc$sExportResults()), value = TRUE)

EProc$sSetLocationInfo(LatDeg = 51.0, LongDeg = 13.6, TimeZoneHour = 1)
EProc$sMDSGapFill('Tair', FillAll = FALSE, minNWarnRunLength = NA)
EProc$sMDSGapFill('Rg', FillAll = FALSE, minNWarnRunLength = NA)
EProc$sMDSGapFill('VPD', FillAll = FALSE, minNWarnRunLength = NA)
EProc$sMRFluxPartitionUStarScens()
grep("GPP_.*_f$",names(EProc$sExportResults()), value = TRUE)
if (FALSE) {
  # run only interactively, because it takes long
  EProc$sGLFluxPartitionUStarScens(uStarScenKeep = "U50")
  grep("GPP_DT_.*_f$",names(EProc$sExportResults()), value = TRUE)
}

The argument uStarScenKeep = "U50" specifies that the outputs that are not distinguished by the suffix, e.g. FP_GPP2000, should be reported for the median u* threshold scenario with suffix U50, instead of the default first scenario.

See also

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

REddyProc documentation built on March 18, 2022, 5:41 p.m.