leaf_temperature: Leaf temperature calculation

In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling

Leaf temperature calculation

Description

Campbell & Norman's (1998) leaf temperature calculation based on their equation 14.1 solved using R's root-finding function 'uniroot'. Uses the functions SOLAR_ecto and RADIN_ecto to calculate incoming radiation based on TGRD, TSKY, QSOLR, Z and PDIF. The ectotherm function (and ectoR_devel) can also be used to calculate leaf temperature and is faster and more general (e.g. can simulate different shapes) than the Campbell & Norman function. Both methods are demonstrated in the example for this function. Michael Kearney developed this R function and its sub-function leaf_bal and example in July 2023. Campbell, G. S., & Norman, J. M. (1998). Environmental Biophysics. Springer.

Usage

leaf_temperature(w = 0.1, A = 0.01, A_sil = 0.005, alpha_L = 0.5, alpha_S = 0.85, g_vs_ab = 0.15, g_vs_ad = 0.15, TA = 30, TGRD = 60, TSKY = 10, VEL = 2, RH = 20, QSOLR = 1000, Z = 0, PDIF = 15)

Arguments

w	= 0.1, leaf width, m
A	= 0.01, leaf surface area, m^2
A_sil	= 0.005, leaf silhouette area, m^2
alpha_L	= 0.5, leaf solar absorptivity, -
alpha_S	= 0.8, ground solar absorptivity, -
epsilon_L	= 0.97, leaf emissivity, -
epsilon_sub	= 0.97, substrate emissivity, -
epsilon_sky	= 0.78, sky emissivity, -
g_vs_ab	= 0.5, vapour conductance, abaxial (top of leaf), mol/m2/s
g_vs_ad	= 0, vapour conductance, adaxial (bottom of leaf), mol/m2/s
TA	= 30, air temperature at leaf height from microclimate model, deg C
TGRD	= 60, ground temperature from microclimate model, deg C
TSKY	= 10, sky temperature from microclimate model, deg C
VEL	= 2, wind speed from microclimate model, m/s
RH	= 20, relative humidity from microclimate model, %
QSOLR	= 1000, total horizontal plane solar radiation from microclimate model, W/m2
Z	= 0, solar zenith angle, degrees
PRESS	= 101325, atmospheric pressure, Pa
PDIF	= 0.15, proportion of solar radiation that is diffuse, -
conv_enhance	= 1.4, outdoor convective enhancement factor, Mitchell 1976

Value

leaf temperature (°C)

Examples

library(NicheMapR)

# simulate a microclimate
loc <- c(141.86, -29.05) # outback Australia
micro <<- micro_global(loc = loc, microclima = 1) # setting microclima = 1 to get partitioned diffuse and direct solar - needs internet connection for the DEM download
dates <- micro$dates # mock dates
metout <- as.data.frame(micro$metout) # microclimate aboveground conditions
soil <- as.data.frame(micro$soil) # soil temperature

# obtain relevant microclimate conditions
P_a <- get_pressure(micro$elev/288) # hourlydata$pressure
PRESSs <- rep(P_a, nrow(metout)) # atmospheric pressure, Pa
TAs <- metout$TALOC # air temperature at leaf height from microclimate model, deg C
TGRDs <- soil$D0cm # ground temperature from microclimate model, deg C
TSKYs <- metout$TSKY # sky temperature from microclimate model, deg C
VELs <- metout$VLOC # wind speed from microclimate model, m/s
RHs <- metout$RHLOC # relative humidity from microclimate model, %
QSOLRs <- metout$SOLR # total horizontal plane solar radiation from microclimate model, W/m2
Zs <- metout$ZEN # solar zenith angle, degrees
PDIFs <- micro$diffuse_frac # use variable diffuse fraction
epsilon_sky <- 1 # emissivity has already been incorporated in calculation of TSKYs
alpha_S <- 1 - micro$REF # substrate solar absorptivity

# leaf functional traits required for the heat and water budget
Ww_g <- 1 # wet weight, g
shape <- 2 # 0=plate, 1=cylinder, 2=ellipsoid
g_vs_ab <- 0.3 # leaf vapour conductance, abaxial (bottom of leaf), mol/m2/s
g_vs_ad <- 0.0 # leaf vapour conductance, adaxial (top of leaf), mol/m2/s
g_vs_base <- 0.01 # base leaf vapour conductance when stomata closed, equivalent to 0.1 (µmol H2O) / (m^2 s Pa) from tealeaves
shape_b <- 0.0025 # ratio of b axis:a axis for ellipsoid
shape_c <- 0.1176 # ratio of c axis:a axis for ellipsoid
epsilon_sub <- 0.95 # emissivity of the substrate (-)
epsilon_L <- 0.97 # emissivity of the leaf (-)
alpha_L <- 0.5 # solar absorptivity of the leaf (-)
fatosk <- 0.5 # radiation configuration factor to sky (-)
fatosb <- 0.5 # radiation configuration factor to substrate (-)
conv_enhance <- 1.4 # convective enhancement factor (-)
pct_cond <- 0 # percent of leaf conducting to the ground (%)

# set up vapour conductance vectors and simulate stomatal closure at night
g_vs_abs <- rep(g_vs_ab, nrow(metout))
g_vs_ads <- rep(g_vs_ad, nrow(metout))
g_vs_abs[metout$ZEN == 90] <- 0 # close stomata when the sun is set
g_vs_ads[metout$ZEN == 90] <- 0 # close stomata when the sun is set
g_vs_abs <- g_vs_abs + g_vs_base / 2
g_vs_ads <- g_vs_ads + g_vs_base / 2

# get characteristic dimension and areas using ecto_devel function GEOM_ecto
GEOM.out <- GEOM_ecto(AMASS = Ww_g / 1000, GEOMETRY = shape, SHP = c(1, shape_b, shape_c), PTCOND = pct_cond / 100, PMOUTH = 0, SKINW = 0 / 100)
w <- GEOM.out$AL / 0.7 # leaf width, m
A <- GEOM.out$AREA # total leaf surface area, m2
A_sil <- (GEOM.out$ASILN + GEOM.out$ASILP) / 2 # leaf silhoette area to direct solar radiation, m2

# Campbell and Norman Calculation
T_leaf_CN <- unlist(lapply(1:length(TAs), function(x){leaf_temperature(
  w = w, # leaf width, m
  A = A, # leaf surface area, m^2
  A_sil = A_sil, # leaf silhouette area, m^2
  alpha_L = alpha_L, # leaf solar absorptivity, -
  alpha_S = alpha_S, # ground solar absorptivity, -
  epsilon_L = epsilon_L, # leaf emissivity, -
  epsilon_sub = epsilon_sub, # ground emissivity, -
  epsilon_sky = epsilon_sky, # sky emissivity, -
  g_vs_ab = g_vs_abs[x], # vapour conductance, abaxial (bottom of leaf), mol/m2/s
  g_vs_ad = g_vs_ads[x], # vapour conductance, adaxial (top of leaf), mol/m2/s
  TA = TAs[x], # air temperature at lizard height from microclimate model, deg C
  TGRD = TGRDs[x], # ground temperature from microclimate model, deg C
  TSKY = TSKYs[x], # sky temperature from microclimate model, deg C
  VEL = VELs[x], # wind speed from microclimate model, m/s
  RH = RHs[x], # relative humidity from microclimate model, %
  QSOLR = QSOLRs[x], # total horizontal plane solar radiation from microclimate model, W/m2
  Z = Zs[x], # solar zenith angle from microclimate model, degrees
  PRESS = PRESSs[x],
  PDIF = PDIFs[x], # proportion solar radiation that is diffuse, -
  conv_enhance = conv_enhance # convective enhancement factor
)})) # run leaf_temperature across environments

month <- 1 # choose a month to plot
sub <- which(floor(dates) + 1 == month)
T_air_2m <- metout$TAREF
T_air_1cm <- metout$TALOC
plot(T_air_1cm[sub], type = 'l', col = 'blue', ylab = 'temperature, deg C', xlab = 'hour of day', ylim = c(15, 50))
points(T_air_2m[sub], type = 'l', col = 'blue', lty = 2)
points(T_leaf_CN[sub], type = 'l')

# compare to ectotherm model calculation

# model settings
live <- 0 # don't simulate behaviour or respiration
leaf <- 1 # use the stomatal conductance formulation for evaporation
postur <- 0 # no postural behaviour

ecto <- ectotherm(leaf = leaf,
                  pct_wet = 0,
                  g_vs_ab = g_vs_abs,
                  g_vs_ad = g_vs_ads,
                  preshr = PRESSs,
                  PDIF = PDIFs,
                  conv_enhance = conv_enhance,
                  Ww_g = Ww_g,
                  alpha_max = alpha_L,
                  alpha_min = alpha_L,
                  fatosk = fatosk,
                  fatosb = fatosb,
                  epsilon_sub = epsilon_sub,
                  epsilon = epsilon_L,
                  shape_b = shape_b,
                  shape_c = shape_c,
                  live = live,
                  pct_cond = pct_cond,
                  shape = shape,
                  postur = postur)
environ <- as.data.frame(ecto$environ)
T_leaf_NMR <- environ$TC

points(T_leaf_NMR[sub], type = 'l', lty = 2)
legend(x = 3, y = 50, legend = c("T_air 1.2m", "T_air 1cm", "T_leaf_CN", "T_leaf_NMR"), col = c('blue', 'blue', 'black', 'black'), lty = c(2, 1, 1, 2), bty = "n")

mrke/NicheMapR documentation built on April 3, 2024, 10:05 a.m.