# 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$set(eval = !is_check)
#rmarkdown::render("vignettes/bigleaf.Rmd")
knitr::opts_knit$set(root.dir = '..')
knitr::opts_chunk$set(
    #, fig.align = "center"
    #, fig.width = 3.27, fig.height = 2.5, dev.args = list(pointsize = 10)
    #,cache = TRUE
    #, fig.width = 4.3, fig.height = 3.2, dev.args = list(pointsize = 10)
    #, fig.width = 6.3, fig.height = 6.2, dev.args = list(pointsize = 10)
    # works with html but causes problems with latex
    #,out.extra = 'style = "display:block; margin: auto"' 
    )
knitr::knit_hooks$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))
#bgiDir <- "~/bgi"

bigleaf package replacing GeoFunctions of REddyProc

REddyProc package included several utility functions that were somewhat out of the package scope. These functions are removed from package.

This vignette shows how to replace them by functions from the bigleaf package.

if (!require("bigleaf", quietly = TRUE)) stop(
  "bigleaf package must be installed to create this vignette.")
library(REddyProc)

Vapour pressure deficit (VPD)

Vapour pressure deficit (VPD) was computed with REddyProc in $hPa$ from relative humidity in $\%$ and air temperature in $^{\circ}C$.

VPD0 <- fCalcVPDfromRHandTair(DEGebExample$rH, DEGebExample$Tair)

bigleaf package computes VPD in $kPa$ and requires relative humidity as fraction .

VPD.hPa <- rH.to.VPD(DEGebExample$rH/100, DEGebExample$Tair)*10

Saturation vapor pressure (SVP) or eSat in $hPa$ was computed from air temperature.

Tair <- seq(10,25,by = 5)
eSat0 <- fCalcSVPfromTair(Tair)

is replaced by Esat.slope which uses $kPa$ as pressure unit:

(eSat <- Esat.slope(Tair)$Esat * 10)

Actual vapor pressure (AVP) or e in $hPa$ was also computed from Vapor mole fraction (VMF) in $mol/mol$ and pressure in $hPa$.

VMF <- seq(0.01,0.03,by = 0.005)
press.in.hPa <- 1000 
e0 <- fCalcAVPfromVMFandPress(VMF, press.in.hPa)

There is no replacement function, as this is just the multiplication of the two arguments.

(e <- VMF * press.in.hPa)

Relative humidity (rH) in $\%$ was computed from AVP in $hPa$ and temperature.

e.in.hPa <- seq(0,30,by = 5)
Tair <- 25           
(rH0 <- fCalcRHfromAVPandTair(e.in.hPa, Tair))

Again this is replaced by a function using pressure units $kPa$ and relative humidity as fraction.

(rH <- e.to.rH(e.in.hPa/10, Tair)*100)

Evapotranspiration from latent heat and air temperature

LE <- seq(300,500,by = 50)
Tair <- 25
ET0 <- fCalcETfromLE(LE, Tair)

The corresponding bigleaf function LE.to.ET returns a value in kg/m2/s. This needs to be converted to mmol/m2/s as returned by the former fCalcETfromLE.

ETkg <- LE.to.ET(LE, Tair)
(ETmmol <- kg.to.mol(ETkg)*1000)

Converting visible radiation from irradiance to photons flux

Photon flux density (PPFD) of visible light can be computed from energy in incoming radiation

Rg <- 200

bigleaf function Rg.to.PPFD combines the two former REddyProc functions fConvertVisibleWm2toPhotons and fConvertGlobalToVisible.

PPFDVis0 <- fConvertGlobalToVisible(fConvertVisibleWm2toPhotons(Rg))
(PPFDVis <- Rg.to.PPFD(Rg))

The PPFD of light including non-visible parts, i.e. former fConvertVisibleWm2toPhotons, is obtained by setting argument frac_PAR to 1.

(PPFDAll <- Rg.to.PPFD(Rg, frac_PAR = 1))

Potential and Extraterrestrial solar radiation

Potential radiation ($W m^{-2}$) depends on time and geo-location.

doy <- 160
hour <- seq(6,18,by = 0.2)
latDeg <- 39.94
longDeg <- -5.77
timezone <- +1

Formerly, REddyProc provided:

(potRad0 <- fCalcPotRadiation(doy, hour, latDeg, longDeg, timezone))

This is replaced by bigleaf:

head(potRad <- potential.radiation(doy, hour, latDeg, longDeg, timezone))

Extraterrestrial solar radiation was formerly computed by REddyProc by:

(extRad0 <- fCalcExtRadiation(doy))

This is replaced by bigleaf:

(extRad <- extraterrestrial.radiation(doy))

Required computation of sun position (computeSunPosition) and difference between apparent local time time and time zone time (computeSolarToLocalTimeDifference) have been moved to package solartime.



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REddyProc documentation built on March 18, 2020, 9:07 a.m.