Nothing
## ----include = FALSE----------------------------------------------------------
# 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$set(eval = !is_check)
## ----setup, include = FALSE---------------------------------------------------
library(knitr)
# rmarkdown::render("vignettes/DEGebExample.Rmd")
opts_chunk$set(out.extra = 'style = "display:block; margin: auto"'
#, fig.align = "center"
, fig.width = 4.3, fig.height = 3.2, dev.args = list(pointsize = 10)
, message = FALSE
)
knit_hooks$set(spar = function(before, options, envir) {
if (before) {
par( las = 1 ) #also y axis labels horizontal
par(mar = c(2.0,3.3,0,0) + 0.3 ) #margins
par(tck = 0.02 ) #axe-tick length inside plots
par(mgp = c(1.1,0.2,0) ) #positioning of axis title, axis labels, axis
}
})
# genVigs("DEGebExample")
## ----results = 'hide'---------------------------------------------------------
#isDevelopMode <- TRUE
if (!exists("isDevelopMode")) library(REddyProc)
set.seed(0815) # for reproducible results
## -----------------------------------------------------------------------------
data(DEGebExample)
summary(DEGebExample)
## -----------------------------------------------------------------------------
DEGebExample$VPD <- fCalcVPDfromRHandTair(DEGebExample$rH, DEGebExample$Tair)
EProc <- sEddyProc$new('DE-Geb', DEGebExample, c('NEE','Rg','Tair','VPD', 'Ustar'))
EProc$sSetLocationInfo(LatDeg = 51.1, LongDeg = 10.9, TimeZoneHour = 1) #Location of Gebesee
## ----DEGeb_estUStar1a, spar = TRUE, fig.width = 10----------------------------
seasonStarts <- as.data.frame( do.call( rbind, list(
c(70,2004)
,c(210,2004)
,c(320,2004)
,c(70,2005)
,c(180,2005)
,c(320,2005)
,c(120,2006)
,c(305,2006)
)))
seasonFactor <- usCreateSeasonFactorYdayYear(
DEGebExample$DateTime - 15*60, starts = seasonStarts)
plot( NEE ~ DateTime, DEGebExample )
seasonStartsDate <- fConvertTimeToPosix( data.frame(Year = seasonStarts[,2]
, DoY = seasonStarts[,1], Hour = 0.25), 'YDH'
, Year = "Year", Day = "DoY", Hour = "Hour")
abline( v = seasonStartsDate$DateTime)
## ----DEGeb_estUStar1b, cache = TRUE-------------------------------------------
(uStarTh <- EProc$sEstUstarThold(seasonFactor = seasonFactor))
#EProc$useSeaonsalUStarThresholds()
# estimation can be inspected by plotting the saturation of NEE with UStar
# for the temperatures of one season
#EProc$sPlotNEEVersusUStarForSeason( levels(uStarTh$season)[2] )
## ----DEGeb_estUStar1c---------------------------------------------------------
EProc$useSeaonsalUStarThresholds()
EProc$sGetUstarScenarios()
## ----DEGeb_gapFill1, cache = TRUE, eval = FALSE, output = 'hide', message = FALSE----
# EProc$sMDSGapFillAfterUstar('NEE', FillAll = FALSE, isVerbose = FALSE)
## ----DEGeb_estUStarBoot1, cache = TRUE, message = FALSE-----------------------
EProc <- sEddyProc$new('DE-Geb', DEGebExample, c('NEE','Rg','Tair','VPD', 'Ustar'))
EProc$sSetLocationInfo(LatDeg = 51.1, LongDeg = 10.9, TimeZoneHour = 1) #Location of Gebesee
# here, because of processing time only 30 samples instead of 100, and 10% and 90%
# percentile instead of default 5%,50%, and 95% with 100 samples
EProc$sEstimateUstarScenarios(
seasonFactor = seasonFactor, nSample = 30L, probs = c(0.1,0.9))
#(uStarScens <- usGetSeasonalSeasonUStarMap(
# EProc$sGetEstimatedUstarThresholdDistribution()
#))
#EProc$sSetUstarScenarios(uStarScens)
EProc$useSeaonsalUStarThresholds()
EProc$sGetUstarScenarios()
## ----DEGeb_gapFillBoot1, cache = TRUE, message = FALSE, output = 'hide'-------
EProc$sMDSGapFillUStarScens('NEE', FillAll = FALSE)
## -----------------------------------------------------------------------------
grep("^NEE.*_f$", colnames( EProc$sExportResults()), value = TRUE )
## ----DEGeb_fluxPart1, cache = TRUE, message = FALSE---------------------------
EProc$sMDSGapFill('Tair', FillAll = FALSE)
EProc$sApplyUStarScen( EProc$sMRFluxPartition )
#grep("U10", colnames(EProc$sExportResults()), value = TRUE)
grep("^GPP.*_f$", colnames( EProc$sExportResults()), value = TRUE )
## ----DEGeb_estUStarCPT, cache = TRUE------------------------------------------
EProc <- sEddyProc$new(
'DE-Geb', DEGebExample, c('NEE','Rg','Tair','VPD', 'Ustar'))
resUStar <- EProc$sEstUstarThold(
ctrlUstarEst = usControlUstarEst(isUsingCPTSeveralT = TRUE)
, seasonFactor = seasonFactor
)
#(uStarThCP <- usGetSeasonalSeasonUStarMap(resUStar))
EProc$useSeaonsalUStarThresholds()
EProc$sGetUstarScenarios()
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