medfate (version 0.8.2)

light: Light extinction and absortion functions

Description

Functions light_layerIrradianceFraction and light_layerIrradianceFractionBottomUp calculate the fraction of above-canopy irradiance (and the soil irradiance, respectively) reaching each vegetation layer. Function light_layerSunlitFraction calculates the proportion of sunlit leaves in each vegetation layer. Function light_cohortSunlitShadeAbsorbedRadiation calculates the amount of radiation absorved by cohort and vegetation layers, while differentiating between sunlit and shade leaves.

Usage

light_layerIrradianceFraction(LAIme, LAImd, LAImx, k, alpha, 
                              trunkExtinctionFraction = 0.1)
light_layerIrradianceFractionBottomUp(LAIme, LAImd, LAImx, k, alpha, 
                              trunkExtinctionFraction = 0.1)
light_layerSunlitFraction(LAIme, LAImd, kb)
light_cohortSunlitShadeAbsorbedRadiation(Ib0, Id0, Ibf, Idf, beta,
                                         LAIme, LAImd,
                                         kb, kd, alpha, gamma)
light_instantaneousLightExtinctionAbsortion(LAIme, LAImd, LAImx, 
                                            kPAR, gammaSWR,
                                            ddd, LWR_diffuse,
                                            ntimesteps = 24, canopyMode= "sunshade", 
                                            trunkExtinctionFraction = 0.1)

Arguments

LAIme

A numeric matrix of live expanded LAI values per vegetation layer (row) and cohort (column).

LAImd

A numeric matrix of dead LAI values per vegetation layer (row) and cohort (column).

LAImx

A numeric matrix of maximum LAI values per vegetation layer (row) and cohort (column).

k

A vector of light extinction coefficients.

kb

A vector of direct light extinction coefficients.

kd

A vector of diffuse light extinction coefficients.

Ib0

Above-canopy direct incident radiation.

Id0

Above-canopy diffuse incident radiation.

Ibf

Fraction of above-canopy direct radiation reaching each vegetation layer.

Idf

Fraction of above-canopy diffuse radiation reaching each vegetation layer.

alpha

A vecfor of leaf absorvance by species.

beta

Solar elevation (in radians).

gamma

Vector of canopy reflectance values.

kPAR

A vector of visible light extinction coefficients for each cohort.

gammaSWR

A vector of short-wave reflectance coefficients (albedo) for each cohort.

ddd

A dataframe with direct and diffuse radiation for different subdaily time steps (see function radiation_directDiffuseDay in package meteoland).

LWR_diffuse

A vector with diffuse longwave radiation for different subdaily time steps.

ntimesteps

Number of subdaily time steps.

canopyMode

Indicates how crowns should be described to calculate photosynthesis/extinction. Accepted values are "sunshade" (distinguishes photosynthesis in sun leaves from shade leaves) and "multilayer" (distinguishes photosynthesis of sun leaves and shade leaves in each canopy layer).

trunkExtinctionFraction

Fraction of extinction due to trunks (for winter deciduous forests).

Value

Functions light_layerIrradianceFraction, light_layerIrradianceFractionBottomUp and light_layerSunlitFraction return a numeric vector of length equal to the number of vegetation layers. Function light_cohortSunlitShadeAbsorbedRadiation returns a list with two elements (matrices): I_sunlit and I_shade.

Details

Function codification adapted from Anten & Bastiaans (2016). Vegetation layers are assumed to be ordered from bottom to top.

References

Anten, N.P.R., Bastiaans, L., 2016. The use of canopy models to analyze light competition among plants, in: Hikosaka, K., Niinemets, U., Anten, N.P.R. (Eds.), Canopy Photosynthesis: From Basics to Application. Springer, pp. 379<U+2013>398.

See Also

spwb

Examples

# NOT RUN {
LAI = 2
nlayer = 10
LAIlayerlive = matrix(rep(LAI/nlayer,nlayer),nlayer,1)
LAIlayerdead = matrix(0,nlayer,1)
kb = 0.8
kd_PAR = 0.5
kd_SWR = kd_PAR/1.35
alpha_PAR = 0.9
gamma_PAR = 0.04
gamma_SWR = 0.05
alpha_SWR = 0.7

Ibfpar = light_layerIrradianceFraction(LAIlayerlive,LAIlayerdead,LAIlayerlive,kb, alpha_PAR)
Idfpar = light_layerIrradianceFraction(LAIlayerlive,LAIlayerdead,LAIlayerlive,kd_PAR, alpha_PAR)
Ibfswr = light_layerIrradianceFraction(LAIlayerlive,LAIlayerdead,LAIlayerlive,kb, alpha_SWR)
Idfswr = light_layerIrradianceFraction(LAIlayerlive,LAIlayerdead,LAIlayerlive,kd_SWR, alpha_SWR)
fsunlit = light_layerSunlitFraction(LAIlayerlive, LAIlayerdead, kb)
SHarea = (1-fsunlit)*LAIlayerlive[,1] 
SLarea = fsunlit*LAIlayerlive[,1] 

par(mar=c(4,4,1,1), mfrow=c(1,2))
plot(Ibfpar*100, 1:nlayer,type="l", ylab="Layer", 
     xlab="Percentage of irradiance", xlim=c(0,100), ylim=c(1,nlayer), col="dark green")
lines(Idfpar*100, 1:nlayer, col="dark green", lty=2)
lines(Ibfswr*100, 1:nlayer, col="red")
lines(Idfswr*100, 1:nlayer, col="red", lty=2)

plot(fsunlit*100, 1:nlayer,type="l", ylab="Layer", 
     xlab="Percentage of leaves", xlim=c(0,100), ylim=c(1,nlayer))
lines((1-fsunlit)*100, 1:nlayer, lty=2)


solarElevation = 0.67
SWR_direct = 1100
SWR_diffuse = 300
PAR_direct = 550
PAR_diffuse = 150


abs_PAR = light_cohortSunlitShadeAbsorbedRadiation(PAR_direct, PAR_diffuse,
                        Ibfpar, Idfpar, beta = solarElevation, 
                        LAIlayerlive, LAIlayerdead, kb, kd_PAR, alpha_PAR, gamma_PAR)
abs_SWR = light_cohortSunlitShadeAbsorbedRadiation(SWR_direct, SWR_diffuse,
                        Ibfswr, Idfswr, beta = solarElevation, 
                        LAIlayerlive, LAIlayerdead, kb, kd_SWR, alpha_SWR, gamma_SWR)
par(mar=c(4,4,1,1), mfrow=c(1,2))
absRadSL = abs_SWR$I_sunlit[,1]
absRadSH = abs_SWR$I_shade[,1]
lambda = 546.6507
QSL = abs_PAR$I_sunlit[,1]*lambda*0.836*0.01
QSH = abs_PAR$I_shade[,1]*lambda*0.836*0.01
plot(QSL, 1:nlayer,type="l", ylab="Layer", 
     xlab="Absorbed PAR quantum flux per leaf area", ylim=c(1,nlayer), col="dark green", 
     xlim=c(0,max(QSL)))
lines(QSH, 1:nlayer, col="dark green", lty=2)
plot(absRadSL, 1:nlayer,type="l", ylab="Layer", 
     xlab="Absorbed SWR per leaf area (W/m2)", ylim=c(1,nlayer), col="red", 
     xlim=c(0,max(absRadSL)))
lines(absRadSH, 1:nlayer, col="red", lty=2)

# }