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cropbox-plants2020.jl
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cropbox-plants2020.jl
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# -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# formats: ipynb,jl:light
# text_representation:
# extension: .jl
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.6.0
# kernelspec:
# display_name: Julia 1.5.2
# language: julia
# name: julia-1.5
# ---
using Cropbox
using CSV
using DataFrames
using DataFramesMeta
using Statistics
using GLM
import Gadfly
import Cairo
using Logging
Logging.disable_logging(Logging.Warn)
# ## Dataset
# We have two datasets from an experiment conducted in 2005 with maize plots under multiple levels of nitrogen application.
#
# - `corn2005spad.csv`: overal growth data including SPAD
# - `corn2005ge.csv`: corresponding gas exchange measurements from LI-COR
# ### SPAD
obs_spad = CSV.read("corn2005spad.csv") |> unitfy
plot(obs_spad, :SPAD, :leaf_N, kind=:scatter)
plot(obs_spad, :leaf_N, :A_max, kind=:scatter)
plot(obs_spad, :nitrogen, :leaf_N, kind=:scatter)
# ### Gas Exchange
obs_ge = CSV.read("corn2005ge.csv") |> unitfy
# Recalculate stomatal conductance in units that our model uses for taking account air pressure.
obs_ge.gs = obs_ge.Cond ./ obs_ge.Press .|> u"mol/m^2/s/bar";
# Make a combined dataset.
obs = join(obs_ge, obs_spad, on=[:plot, :subplot], makeunique=true);
# ## Model
# Gas exchange model is mostly derived from MAIZSIM, adapting to Cropbox framework.
# ### SPAD - N
@system Nitrogen begin
SPAD: SPAD_greenness ~ preserve(parameter)
SNa: SPAD_N_coeff_a ~ preserve(u"g/m^2", parameter)
SNb: SPAD_N_coeff_b ~ preserve(u"g/m^2", parameter)
SNc: SPAD_N_coeff_c ~ preserve(u"g/m^2", parameter)
N(SPAD, a=SNa, b=SNb, c=SNc): leaf_nitrogen_content => begin
a*SPAD^2 + b*SPAD + c
end ~ preserve(u"g/m^2", parameter)
Np(N, SLA) => N * SLA ~ track(u"percent")
SLA: specific_leaf_area => 200 ~ preserve(u"cm^2/g")
end
@system NitrogenController(Nitrogen, Controller)
spad_configs = [:Nitrogen => :SPAD => x for x in obs_spad.SPAD]
nitrogen_config = :Nitrogen => (SNa=0.0004, SNb=0.0120, SNc=0)
# We have a quadratic relationship $N = 0.0004S^2 + 0.0120S$. Note that intercept (`SNc`) is close to zero.
est = simulate(NitrogenController, [(index=:SPAD, target=:N)], [(c, nitrogen_config) for c in spad_configs], skipfirst=true)[1]
p = plot(obs_spad, :SPAD, :leaf_N, ylab="Leaf nitrogen", name="Observed", legendpos=(0.1,-0.3), kind=:scatter)
plot!(p, est, :SPAD, :N, name="Fitted (R^2=0.92)", kind=:line)
p' |> Gadfly.PDF("SPAD-N.pdf")
p
lm(@formula(est ~ obs), DataFrame(obs=deunitfy(obs_spad.leaf_N), est=deunitfy(est.N))) |> r2
# ### Environment
@system VaporPressure begin
a => 0.611 ~ preserve(u"kPa", parameter)
b => 17.502 ~ preserve(parameter)
c => 240.97 ~ preserve(parameter)
es(a, b, c; T(u"°C")): saturation => (t = deunitfy(T); a*exp((b*t)/(c+t))) ~ call(u"kPa")
ea(es; T(u"°C"), RH(u"percent")): ambient => es(T) * RH ~ call(u"kPa")
D(es; T(u"°C"), RH(u"percent")): deficit => es(T) * (1 - RH) ~ call(u"kPa")
RH(es; T(u"°C"), VPD(u"kPa")): relative_humidity => 1 - VPD / es(T) ~ call(u"NoUnits")
Δ(es, b, c; T(u"°C")): saturation_slope_delta => (e = es(T); t = deunitfy(T); e*(b*c)/(c+t)^2 / u"K") ~ call(u"kPa/K")
s(Δ; T(u"°C"), P(u"kPa")): saturation_slope => Δ(T) / P ~ call(u"K^-1")
end
@system Weather begin
vp(context): vapor_pressure ~ ::VaporPressure
PFD: photon_flux_density ~ preserve(u"μmol/m^2/s", parameter)
CO2: carbon_dioxide ~ preserve(u"μmol/mol", parameter)
RH: relative_humidity ~ preserve(u"percent", parameter)
T_air: air_temperature ~ preserve(u"°C", parameter)
Tk_air(T_air): absolute_air_temperature ~ track(u"K")
wind: wind_speed ~ preserve(u"m/s", parameter)
P_air: air_pressure => 100 ~ preserve(u"kPa", parameter)
VPD(T_air, RH, D=vp.D): vapor_pressure_deficit => D(T_air, RH) ~ track(u"kPa")
VPD_Δ(T_air, Δ=vp.Δ): vapor_pressure_saturation_slope_delta => Δ(T_air) ~ track(u"kPa/K")
VPD_s(T_air, P_air, s=vp.s): vapor_pressure_saturation_slope => s(T_air, P_air) ~ track(u"K^-1")
end
@system Diffusion begin
Dw: diffusion_coeff_for_water_vapor_in_air_at_20 => 24.2 ~ preserve(u"mm^2/s", parameter)
Dc: diffusion_coeff_for_co2_in_air_at_20 => 14.7 ~ preserve(u"mm^2/s", parameter)
Dh: diffusion_coeff_for_heat_in_air_at_20 => 21.5 ~ preserve(u"mm^2/s", parameter)
Dm: diffusion_coeff_for_momentum_in_air_at_20 => 15.1 ~ preserve(u"mm^2/s", parameter)
end
@system Irradiance begin
PFD ~ hold
PPFD(PFD): photosynthetic_photon_flux_density ~ track(u"μmol/m^2/s")
δ: leaf_scattering => 0.15 ~ preserve(parameter)
f: leaf_spectral_correction => 0.15 ~ preserve(parameter)
Ia(PPFD, δ): absorbed_irradiance => begin
PPFD * (1 - δ)
end ~ track(u"μmol/m^2/s")
I2(Ia, f): effective_irradiance => begin
Ia * (1 - f) / 2
end ~ track(u"μmol/m^2/s")
end
# ### C4
@system TemperatureDependence begin
T: leaf_temperature ~ hold
Tk(T): absolute_leaf_temperature ~ track(u"K")
Tb: base_temperature => 25 ~ preserve(u"°C", parameter)
Tbk(Tb): absolute_base_temperature ~ preserve(u"K")
kT(T, Tk, Tb, Tbk; Ea(u"kJ/mol")): arrhenius_equation => begin
exp(Ea * (T - Tb) / (u"R" * Tk * Tbk))
end ~ call
kTpeak(Tk, Tbk, kT; Ea(u"kJ/mol"), S(u"J/mol/K"), H(u"kJ/mol")): peaked_function => begin
R = u"R"
kT(Ea) * (1 + exp((S*Tbk - H) / (R*Tbk))) / (1 + exp((S*Tk - H) / (R*Tk)))
end ~ call
Q10 => 2 ~ preserve(parameter)
kTQ10(T, Tb, Q10): q10_rate => begin
Q10^((T - Tb) / 10u"K")
end ~ track
end
@system NitrogenDependence begin
N: leaf_nitrogen_content ~ hold
s => 2.9 ~ preserve(u"m^2/g", parameter)
N0 => 0.25 ~ preserve(u"g/m^2", parameter)
kN(N, s, N0): nitrogen_limited_rate => begin
2 / (1 + exp(-s * (max(N0, N) - N0))) - 1
end ~ track
end
@system CBase(TemperatureDependence, NitrogenDependence) begin
Ci: intercellular_co2 ~ hold
I2: effective_irradiance ~ hold
end
@system C4Base(CBase) begin
Cm(Ci): mesophyll_co2 ~ track(u"μbar")
gbs: bundle_sheath_conductance => 0.003 ~ preserve(u"mol/m^2/s/bar", parameter)
end
@system C4c(C4Base) begin
Kp25: pep_carboxylase_constant_for_co2_at_25 => 80 ~ preserve(u"μbar", parameter)
Kp(Kp25, kTQ10): pep_carboxylase_constant_for_co2 => begin
Kp25 * kTQ10
end ~ track(u"μbar")
Vpm25: maximum_pep_carboxylation_rate_for_co2_at_25 => 70 ~ preserve(u"μmol/m^2/s", parameter)
EaVp: activation_energy_for_pep_carboxylation => 75.1 ~ preserve(u"kJ/mol", parameter)
Vpmax(Vpm25, kT, EaVp, kN): maximum_pep_carboxylation_rate => begin
Vpm25 * kT(EaVp) * kN
end ~ track(u"μmol/m^2/s")
Vpr25: regeneration_limited_pep_carboxylation_rate_for_co2_at_25 => 80 ~ preserve(u"μmol/m^2/s", parameter)
Vpr(Vpr25, kTQ10): regeneration_limited_pep_carboxylation_rate => begin
Vpr25 * kTQ10
end ~ track(u"μmol/m^2/s")
Vp(Vpmax, Vpr, Cm, Kp): pep_carboxylation_rate => begin
(Cm * Vpmax) / (Cm + Kp)
end ~ track(u"μmol/m^2/s", max=Vpr)
Vcm25: maximum_carboxylation_rate_at_25 => 50 ~ preserve(u"μmol/m^2/s", parameter)
EaVc: activation_energy_for_carboxylation => 55.9 ~ preserve(u"kJ/mol", parameter)
Vcmax(Vcm25, kT, EaVc, kN): maximum_carboxylation_rate => begin
Vcm25 * kT(EaVc) * kN
end ~ track(u"μmol/m^2/s")
end
@system C4j(C4Base) begin
Jm25: maximum_electron_transport_rate_at_25 => 300 ~ preserve(u"μmol/m^2/s", parameter)
Eaj: activation_energy_for_electron_transport => 32.8 ~ preserve(u"kJ/mol", parameter)
Sj: electron_transport_temperature_response => 702.6 ~ preserve(u"J/mol/K", parameter)
Hj: electron_transport_curvature => 220 ~ preserve(u"kJ/mol", parameter)
Jmax(Jm25, kTpeak, Eaj, Sj, Hj, kN): maximum_electron_transport_rate => begin
Jm25 * kTpeak(Eaj, Sj, Hj) * kN
end ~ track(u"μmol/m^2/s")
θ: light_transition_sharpness => 0.5 ~ preserve(parameter)
J(I2, Jmax, θ): electron_transport_rate => begin
a = θ
b = -(I2+Jmax)
c = I2*Jmax
a*J^2 + b*J + c ⩵ 0
end ~ solve(lower=0, upper=Jmax, u"μmol/m^2/s")
end
@system C4r(C4Base) begin
Kc25: rubisco_constant_for_co2_at_25 => 650 ~ preserve(u"μbar", parameter)
Eac: activation_energy_for_co2 => 59.4 ~ preserve(u"kJ/mol", parameter)
Kc(kT, Kc25, Eac): rubisco_constant_for_co2 => begin
Kc25 * kT(Eac)
end ~ track(u"μbar")
Ko25: rubisco_constant_for_o2_at_25 => 450 ~ preserve(u"mbar", parameter)
# Activation energy for Ko, Bernacchi (2001)
Eao: activation_energy_for_o2 => 36 ~ preserve(u"kJ/mol", parameter)
Ko(Ko25, kT, Eao): rubisco_constant_for_o2 => begin
Ko25 * kT(Eao)
end ~ track(u"mbar")
Om: mesophyll_o2_partial_pressure => 210 ~ preserve(u"mbar", parameter)
Km(Kc, Om, Ko): rubisco_constant_for_co2_with_o2 => begin
Kc * (1 + Om / Ko)
end ~ track(u"μbar")
Rd25: dark_respiration_at_25 => 2 ~ preserve(u"μmol/m^2/s", parameter)
Ear: activation_energy_for_respiration => 39.8 ~ preserve(u"kJ/mol", parameter)
Rd(Rd25, kT, Ear): dark_respiration => begin
Rd25 * kT(Ear)
end ~ track(u"μmol/m^2/s")
Rm(Rd) => 0.5Rd ~ track(u"μmol/m^2/s")
end
@system C4Rate(C4c, C4j, C4r) begin
Ac1(Vp, gbs, Cm, Rm) => (Vp + gbs*Cm - Rm) ~ track(u"μmol/m^2/s")
Ac2(Vcmax, Rd) => (Vcmax - Rd) ~ track(u"μmol/m^2/s")
Ac(Ac1, Ac2): enzyme_limited_photosynthesis_rate => begin
min(Ac1, Ac2)
end ~ track(u"μmol/m^2/s")
x: electron_transport_partitioning_factor => 0.4 ~ preserve(parameter)
Aj1(x, J, Rm, gbs, Cm) => (x * J/2 + gbs*Cm - Rm) ~ track(u"μmol/m^2/s")
Aj0(x, J, Rm, gbs, Cm) => (x * J/2 - gbs*Cm - Rm) ~ track(u"μmol/m^2/s")
Aj2(x, J, Rd) => (1-x) * J/3 - Rd ~ track(u"μmol/m^2/s")
Aj(Aj1, Aj2): transport_limited_photosynthesis_rate => begin
min(Aj1, Aj2)
end ~ track(u"μmol/m^2/s")
β: photosynthesis_transition_factor => 0.99 ~ preserve(parameter)
A_net(Ac, Aj, β): net_photosynthesis => begin
x = A_net
a = β
b = -(Ac+Aj)
c = Ac*Aj
a*x^2 + b*x + c ⩵ 0
end ~ solve(pick=:minimum, u"μmol/m^2/s")
A_gross(A_net, Rd): gross_photosynthesis => begin
A_gross = A_net + Rd
end ~ track(u"μmol/m^2/s")
end
@system C4(C4Rate)
# ### Interface
# #### Boundary Layer
@system BoundaryLayer(Weather, Diffusion) begin
w: leaf_width => 10 ~ preserve(u"cm", parameter)
sr: stomatal_ratio => 1.0 ~ preserve(parameter)
scr(sr): sides_conductance_ratio => ((sr + 1)^2 / (sr^2 + 1)) ~ preserve
ocr: outdoor_conductance_ratio => 1.4 ~ preserve
u(u=wind): wind_velocity ~ track(u"m/s", min=0.1)
d(w): characteristic_dimension => 0.72w ~ track(u"m")
v(Dm): kinematic_viscosity_of_air ~ preserve(u"m^2/s", parameter)
κ(Dh): thermal_diffusivity_of_air ~ preserve(u"m^2/s", parameter)
Re(u, d, v): reynolds_number => u*d/v ~ track
Nu(Re): nusselt_number => 0.60sqrt(Re) ~ track
gh(κ, Nu, d, scr, ocr, P_air, Tk_air): boundary_layer_heat_conductance => begin
g = κ * Nu / d
g *= scr * ocr
g * P_air / (u"R" * Tk_air)
end ~ track(u"mmol/m^2/s")
rhw(Dw, Dh): ratio_from_heat_to_water_vapor => (Dw / Dh)^(2/3) ~ preserve
gb(rhw, gh, P_air): boundary_layer_conductance => rhw * gh / P_air ~ track(u"mol/m^2/s/bar")
end
# #### Stomata
@system StomataBase(Weather, Diffusion) begin
gs: stomatal_conductance ~ hold
gb: boundary_layer_conductance ~ hold
A_net: net_photosynthesis ~ hold
T: leaf_temperature ~ hold
drb(Dw, Dc): diffusivity_ratio_boundary_layer => (Dw / Dc)^(2/3) ~ preserve(parameter)
dra(Dw, Dc): diffusivity_ratio_air => (Dw / Dc) ~ preserve(parameter)
Ca(CO2, P_air): co2_air => (CO2 * P_air) ~ track(u"μbar")
Cs(Ca, A_net, gbc): co2_at_leaf_surface => begin
Ca - A_net / gbc
end ~ track(u"μbar")
gv(gs, gb): total_conductance_h2o => (gs * gb / (gs + gb)) ~ track(u"mol/m^2/s/bar")
rbc(gb, drb): boundary_layer_resistance_co2 => (drb / gb) ~ track(u"m^2*s/mol*bar")
rsc(gs, dra): stomatal_resistance_co2 => (dra / gs) ~ track(u"m^2*s/mol*bar")
rvc(rbc, rsc): total_resistance_co2 => (rbc + rsc) ~ track(u"m^2*s/mol*bar")
gbc(rbc): boundary_layer_conductance_co2 => (1 / rbc) ~ track(u"mol/m^2/s/bar")
gsc(rsc): stomatal_conductance_co2 => (1 / rsc) ~ track(u"mol/m^2/s/bar")
gvc(rvc): total_conductance_co2 => (1 / rvc) ~ track(u"mol/m^2/s/bar")
end
@system StomataTuzet begin
WP_leaf: leaf_water_potential => 0 ~ preserve(u"MPa", parameter)
Ψv(WP_leaf): bulk_leaf_water_potential ~ track(u"MPa")
Ψf: reference_leaf_water_potential => -1.2 ~ preserve(u"MPa", parameter)
sf: stomata_sensitivity_param => 2.3 ~ preserve(u"MPa^-1", parameter)
fΨv(Ψv, Ψf, sf): stomata_sensitivty => begin
(1 + exp(sf*Ψf)) / (1 + exp(sf*(Ψf-Ψv)))
end ~ track
end
# ##### Ball-Berry Model
@system StomataBallBerry(StomataBase, StomataTuzet) begin
g0 => 0.017 ~ preserve(u"mol/m^2/s/bar", parameter)
g1 => 4.53 ~ preserve(parameter)
hs(g0, g1, gb, A_net, Cs, fΨv, RH): relative_humidity_at_leaf_surface => begin
gs = g0 + g1*(A_net*hs/Cs) * fΨv
(hs - RH)*gb ⩵ (1 - hs)*gs
end ~ solve(lower=0, upper=1)
Ds(D=vp.D, T, hs): vapor_pressure_deficit_at_leaf_surface => begin
D(T, hs)
end ~ track(u"kPa")
gs(g0, g1, A_net, hs, Cs, fΨv): stomatal_conductance => begin
g0 + g1*(A_net*hs/Cs) * fΨv
end ~ track(u"mol/m^2/s/bar", min=g0)
end
# ##### Medlyn Model
@system StomataMedlyn(StomataBase, StomataTuzet) begin
g0 => 0.02 ~ preserve(u"mol/m^2/s/bar", parameter)
g1 => 4.0 ~ preserve(u"√kPa", parameter)
wa(ea=vp.ea, T_air, RH): vapor_pressure_at_air => ea(T_air, RH) ~ track(u"kPa")
wi(es=vp.es, T): vapor_pressure_at_intercellular_space => es(T) ~ track(u"kPa")
ws(Ds, wi): vapor_pressure_at_leaf_surface => (wi - Ds) ~ track(u"kPa")
Ds¹ᐟ²(g0, g1, gb, A_net, Cs, fΨv, wi, wa) => begin
gs = g0 + (1 + g1 / Ds¹ᐟ²) * (A_net / Cs) * fΨv
ws = wi - Ds¹ᐟ²^2
(ws - wa)*gb ⩵ (wi - ws)*gs
end ~ solve(lower=0, upper=√wi', u"√kPa")
Ds(Ds¹ᐟ²): vapor_pressure_deficit_at_leaf_surface => Ds¹ᐟ²^2 ~ track(u"kPa", min=1u"Pa")
hs(RH=vp.RH, T, Ds): relative_humidity_at_leaf_surface => RH(T, Ds) ~ track
gs(g0, g1, A_net, Ds, Cs, fΨv): stomatal_conductance => begin
g0 + (1 + g1/√Ds)*(A_net/Cs) * fΨv
end ~ track(u"mol/m^2/s/bar", min=g0)
end
# #### Intercellular Space
@system IntercellularSpace(Weather) begin
A_net ~ hold
gvc ~ hold
Ca(CO2, P_air): co2_air => (CO2 * P_air) ~ track(u"μbar")
Cimax(Ca): intercellular_co2_upper_limit => 2Ca ~ track(u"μbar")
Cimin: intercellular_co2_lower_limit => 0 ~ preserve(u"μbar")
Ci(Ca, Ci, A_net, gvc): intercellular_co2 => begin
Ca - Ci ⩵ A_net / gvc
end ~ bisect(min=Cimin, upper=Cimax, u"μbar")
end
# ### Energy Balance
@system EnergyBalance(Weather) begin
gv ~ hold
gh ~ hold
PPFD ~ hold
ϵ: leaf_thermal_emissivity => 0.97 ~ preserve(parameter)
σ: stefan_boltzmann_constant => u"σ" ~ preserve(u"W/m^2/K^4")
λ: latent_heat_of_vaporization_at_25 => 44 ~ preserve(u"kJ/mol", parameter)
Cp: specific_heat_of_air => 29.3 ~ preserve(u"J/mol/K", parameter)
k: radiation_conversion_factor => (1 / 4.55) ~ preserve(u"J/μmol")
α_s: absorption_coefficient => 0.79 ~ preserve(parameter)
PAR(PPFD, k): photosynthetically_active_radiation => (PPFD * k) ~ track(u"W/m^2")
R_sw(PAR, α_s): shortwave_radiation_absorbed => (α_s * PAR) ~ track(u"W/m^2")
R_wall(ϵ, σ, Tk_air): thermal_radiation_absorbed_from_wall => 2ϵ*σ*Tk_air^4 ~ track(u"W/m^2")
R_leaf(ϵ, σ, Tk): thermal_radiation_emitted_by_leaf => 2ϵ*σ*Tk^4 ~ track(u"W/m^2")
R_thermal(R_wall, R_leaf): thermal_radiation_absorbed => R_wall - R_leaf ~ track(u"W/m^2")
R_net(R_sw, R_thermal): net_radiation_absorbed => R_sw + R_thermal ~ track(u"W/m^2")
Δw(T, T_air, RH, ea=vp.ambient, es=vp.saturation): leaf_vapor_pressure_gradient => begin
es(T) - ea(T_air, RH)
end ~ track(u"kPa")
E(gv, Δw): transpiration => gv*Δw ~ track(u"mmol/m^2/s")
H(Cp, gh, ΔT): sensible_heat_flux => Cp*gh*ΔT ~ track(u"W/m^2")
λE(λ, E): latent_heat_flux => λ*E ~ track(u"W/m^2")
ΔT(R_net, H, λE): temperature_adjustment => begin
R_net ⩵ H + λE
end ~ bisect(lower=-10, upper=10, u"K", evalunit=u"W/m^2")
T(T_air, ΔT): leaf_temperature => (T_air + ΔT) ~ track(u"°C")
Tk(T): absolute_leaf_temperature ~ track(u"K")
end
# ### Coupling
abstract type GasExchange <: System end
@system GasExchangeBallBerry(
Weather, Nitrogen,
BoundaryLayer, StomataBallBerry, IntercellularSpace, Irradiance, EnergyBalance,
C4, Controller
) <: GasExchange
@system GasExchangeMedlyn(
Weather, Nitrogen,
BoundaryLayer, StomataMedlyn, IntercellularSpace, Irradiance, EnergyBalance,
C4, Controller
) <: GasExchange
h = Cropbox.hierarchy(GasExchangeMedlyn; skipcontext=true)
Cropbox.writeimage("GasExchangeMedlyn.pdf", h)
h
d = Cropbox.dependency(GasExchangeMedlyn)
# Default parameters are mostly from MAIZSIM.
parameters(C4)
# For simplicity, environmental inputs are set as parameters, instead of driving variables loaded from external data frame.
base_config = (
nitrogen_config,
:Nitrogen => (
SPAD = 60,
),
:Weather => (
PFD = 2000,
CO2 = 400,
RH = 66,
T_air = 32,
wind = 2.0,
P_air = 99.4,
),
);
# ## Calibration
# Since our model generally performed well under nitrogen non-limiting condition, we decided to keep the most of existing parameter set and calibrate only a small set of parameters. We will calibrate two parameters (`s`, `N0`) for nitrogen dependency along `A_net` and two parameters (`g0`, `g1`) for stomatal conductance along `gs`.
obs_configs = [(
nitrogen_config,
:Nitrogen => (
SPAD = r[:SPAD],
),
:Weather => (
PFD = r[:PARi],
CO2 = r[:CO2S],
RH = r[:RH_S],
T_air = r[:Tair],
wind = 2.0,
P_air = r[:Press],
),
) for r in eachrow(obs)];
# +
# bb_calib_config = calibrate(GasExchangeBallBerry, obs, obs_configs;
# index=[:PARi => :PFD, :CO2S => :CO2, :RH_S => :RH, :Tair => :T_air, :Press => :P_air, :SPAD],
# target=[:Photo => :A_net, :gs],
# parameters=(
# :NitrogenDependence => (s=(0, 10), N0=(0, 1)),
# :StomataBallBerry => (g0=(0, 1), g1=(0, 10)),
# ),
# skipfirst=true,
# optim=(
# MaxSteps=2000,
# TraceInterval=10,
# RandomizeRngSeed=false,
# ),
# metric=:prmse,
# #weight=[1, 100],
# #pareto=true
# )
# -
bb_calib_config = (
:NitrogenDependence => (s=4.470, N0=0.371),
:StomataBallBerry => (g0=0.036, g1=2.792),
)
# +
# med_calib_config = calibrate(GasExchangeMedlyn, obs, obs_configs;
# index=[:PARi => :PFD, :CO2S => :CO2, :RH_S => :RH, :Tair => :T_air, :Press => :P_air, :SPAD],
# target=[:Photo => :A_net, :gs],
# parameters=(
# :NitrogenDependence => (s=(0, 10), N0=(0, 1)),
# :StomataMedlyn => (g0=(0, 1), g1=(0, 10)),
# ),
# skipfirst=true,
# optim=(
# MaxSteps=2000,
# TraceInterval=10,
# RandomizeRngSeed=false,
# ),
# metric=:prmse,
# #weight=[1, 100],
# #pareto=true
# )
# -
med_calib_config = (
:NitrogenDependence => (s=3.912, N0=0.315),
:StomataMedlyn => (g0=0.031, g1=1.281),
)
bb_med_calib_config = let b=@config(bb_calib_config)[:NitrogenDependence],
m=@config(med_calib_config)[:NitrogenDependence]
(:NitrogenDependence => (s=(b[:s]+m[:s])/2, N0=(b[:N0]+m[:N0])/2),)
end
bb_obs_configs = @config bb_calib_config + obs_configs;
bb_config = (base_config, bb_calib_config, bb_med_calib_config);
med_obs_configs = @config med_calib_config + obs_configs;
med_config = (base_config, med_calib_config, bb_med_calib_config);
# ### Result
visualize_fit(S::Type{<:GasExchange};
configs=[],
obs=obs_ge,
y=:Photo=>:A_net,
title="",
xlab="Observation",
ylab="Model",
pdfname=nothing,
kwargs...
) = begin
p = visualize(obs, S, y; configs=configs, title=title, xlab=xlab, ylab=ylab, name="", kwargs...)
!isnothing(pdfname) && p' |> Gadfly.PDF("$pdfname.pdf")
p' |> Gadfly.SVG()
end
visualize_fit_BB(; configs=bb_obs_configs, kw...) = visualize_fit(GasExchangeBallBerry; configs=configs, kw...)
visualize_fit_MED(; configs=med_obs_configs, kw...) = visualize_fit(GasExchangeMedlyn; configs=configs, kw...)
visualize_fit(; kw...) = visualize_fit_MED(; kw...)
calculate_fit_BB(; configs=bb_obs_configs, kw...) = calculate_fit(GasExchangeBallBerry; configs=configs, kw...)
calculate_fit_MED(; configs=med_obs_configs, kw...) = calculate_fit(GasExchangeMedlyn; configs=configs, kw...)
calculate_fit(S::Type{<:GasExchange};
configs=[],
obs=obs_ge,
y=:Photo=>:A_net,
metric,
stop=nothing, skipfirst=true, filter=nothing,
) = begin
y = y isa Pair ? y : y => y
yo, ye = y
est = simulate(S; configs=configs, stop=stop, skipfirst=skipfirst, filter=filter)
O = obs[yo] |> deunitfy
E = est[ye] |> deunitfy
# Nash-Sutcliffe model efficiency coefficient (NSE)
if metric == :ef
1 - sum((E - O).^2) / sum((O .- mean(O)).^2)
# Willmott's refined index of agreement (d_r)
elseif metric == :dr
let a = sum(abs.(E .- O)),
b = 2sum(abs.(O .- mean(O)))
a <= b ? 1 - a/b : b/a - 1
end
end
end
visualize_fits(maps;
obs=obs_ge,
y=:Photo=>:A_net,
title="",
xlab="Observation",
ylab="Model",
names=nothing,
pdfname=nothing,
kwargs...
) = begin
isnothing(names) && (names = [string(Cropbox.namefor(m.system)) for m in maps])
p = visualize(obs, maps, y; title=title, xlab=xlab, ylab=ylab, names, kwargs...)
!isnothing(pdfname) && p' |> Gadfly.PDF("$pdfname.pdf")
p' |> Gadfly.SVG()
end
# #### Photosynthesis
visualize_fit_BB(y=:Photo=>:A_net, lim=(0,60), #=title="Net Photosynthesis Rate (An)",=# pdfname="fit-BB-An")
calculate_fit_BB(y=:Photo=>:A_net, metric=:dr)
calculate_fit_BB(y=:Photo=>:A_net, metric=:ef)
visualize_fit_MED(y=:Photo=>:A_net, lim=(0,60), #=title="Net Photosynthesis Rate (An)",=# pdfname="fit-MED-An")
calculate_fit_MED(y=:Photo=>:A_net, metric=:dr)
calculate_fit_MED(y=:Photo=>:A_net, metric=:ef)
visualize_fits([
(system=GasExchangeBallBerry, configs=bb_obs_configs),
(system=GasExchangeMedlyn, configs=med_obs_configs),
];
names=["BB (dr=0.879, ef=0.941)", "MED (dr=0.881, ef=0.937)"],
y=:Photo=>:A_net, lim=(0,60),
#legendpos=(0.1,-0.3),
legendpos=(0.5,0.3),
pdfname="fit-BB-MED-An",
)
# #### Stomatal Conductance
visualize_fit_BB(y=:gs, lim=(0,0.65), #=title="Stomatal Conductance (gs)",=# pdfname="fit-BB-gs")
calculate_fit_BB(y=:gs, metric=:dr)
calculate_fit_BB(y=:gs, metric=:ef)
visualize_fit_MED(y=:gs, lim=(0,0.65), #=title="Stomatal Conductance (gs)",=# pdfname="fit-MED-gs")
calculate_fit_MED(y=:gs, metric=:dr)
calculate_fit_MED(y=:gs, metric=:ef)
visualize_fits([
(system=GasExchangeBallBerry, configs=bb_obs_configs),
(system=GasExchangeMedlyn, configs=med_obs_configs),
];
names=["BB (dr=0.804, ef=0.798)", "MED (dr=0.820, ef=0.796)"],
y=:gs, lim=(0,0.65),
legendpos=(0.5,0.3),
pdfname="fit-BB-MED-gs",
)
# #### Temperature
visualize_fit_BB(y=:Tleaf=>:T, lim=(31,36), pdfname="fit-BB-Tl")
calculate_fit_BB(y=:Tleaf=>:T, metric=:dr)
calculate_fit_BB(y=:Tleaf=>:T, metric=:ef)
visualize_fit_MED(y=:Tleaf=>:T, lim=(31,36), pdfname="fit-MED-Tl")
calculate_fit_MED(y=:Tleaf=>:T, metric=:dr)
calculate_fit_MED(y=:Tleaf=>:T, metric=:ef)
visualize_fits([
(system=GasExchangeBallBerry, configs=bb_obs_configs),
(system=GasExchangeMedlyn, configs=med_obs_configs),
];
names=["BB", "MED"],
y=:Tleaf=>:T, lim=(31,36),
legendpos=(0.1,-0.3),
pdfname="fit-BB-MED-T",
)
# ## Analysis
co2_xstep = :Weather => :CO2 => 10:10:1500
visualize_model(S::Type{<:GasExchange};
config=(),
configΔ=(),
x=:Ca,
y=:A_net,
group,
xstep=co2_xstep,
kind=:line,
pdfname=nothing,
kwargs...
) = begin
p = visualize(S, x, y; config=(config, configΔ), group=group, xstep=xstep, kind=kind, kwargs...)
!isnothing(pdfname) && p' |> Gadfly.PDF("$pdfname.pdf")
p' |> Gadfly.SVG()
end
visualize_model_BB(; config=bb_config, kw...) = visualize_model(GasExchangeBallBerry; config=config, kw...)
visualize_model_MED(; config=med_config, kw...) = visualize_model(GasExchangeMedlyn; config=config, kw...)
visualize_model(; kw...) = visualize_model_MED(; kw...)
# ### Ball-Berry vs. Medlyn
# #### Photosynthesis
# ##### Ca
rh_group = :Weather => :RH => 80:-20:20
rh_xstep = :Weather => :RH => 0:1:100
visualize_model_BB(group=rh_group,
x=:Ca, y=:A_net, ylab="An", xlim=(0,1500), ylim=(-10,60), pdfname="BB-Ca-An-RH")
visualize_model_MED(group=rh_group,
x=:Ca, y=:A_net, ylab="An", xlim=(0,1500), ylim=(-10,60), pdfname="MED-Ca-An-RH")
# ##### Ci
visualize_model_BB(group=rh_group,
legendpos=(0.8,0),
x=:Ci, y=:A_net, ylab="An", xlim=(0,600), ylim=(-10,60), pdfname="BB-Ci-An-RH")
visualize_model_BB(group=:Weather=>:RH=>[70,30],
legendpos=(0.8,0), colors=Gadfly.Scale.default_discrete_colors(4)[[1,3]],
x=:Ci, y=:A_net, ylab="An", xlim=(0,600), ylim=(-10,60), pdfname="BB-Ci-An-RH")
visualize_model_MED(group=rh_group,
legendpos=(0.8,0),
x=:Ci, y=:A_net, ylab="An", xlim=(0,600), ylim=(-10,60), pdfname="MED-Ci-An-RH")
visualize_model_MED(group=:Weather=>:RH=>[70,30],
legendpos=(0.8,0), colors=Gadfly.Scale.default_discrete_colors(4)[[1,3]],
x=:Ci, y=:A_net, ylab="An", xlim=(0,600), ylim=(-10,60), pdfname="MED-Ci-An-RH")
# ##### Ta
ta_xstep = :Weather => :T_air => 0:1:50
visualize_model_BB(group=rh_group, xstep=ta_xstep,
legendpos=(0.1,-0.2),
x=:T_air, y=:A_net, xlab="Ta", ylab="An", xlim=(0,50), ylim=(-10,60), pdfname="BB-T-An-RH")
visualize_model_BB(group=rh_group, xstep=ta_xstep,
x=:T_air, y=:Ci, xlab="Ta", xlim=(0,50), ylim=(0,600), pdfname="BB-T-Ci-RH")
visualize_model_BB(group=rh_group, xstep=ta_xstep,
x=:T, y=:Ci, xlab="Tl", xlim=(0,50), ylim=(0,600), pdfname="BB-Tl-Ci-RH")
visualize_model_MED(group=rh_group, xstep=ta_xstep,
legendpos=(0.1,-0.2),
x=:T_air, y=:A_net, xlab="Ta", ylab="An", xlim=(0,50), ylim=(-10,60), pdfname="MED-T-An-RH")
visualize_model_MED(group=rh_group, xstep=ta_xstep,
x=:T_air, y=:Ci, xlab="Ta", xlim=(0,50), ylim=(0,600), pdfname="MED-T-Ci-RH")
visualize_model_MED(group=rh_group, xstep=ta_xstep,
x=:T, y=:Ci, xlab="Tl", xlim=(0,50), ylim=(0,600), pdfname="MED-Tl-Ci-RH")
# ##### RH
visualize_model_BB(group=:Weather=>:CO2=>[1500,800,400,300,200,100], xstep=rh_xstep,
x=:RH, y=:A_net, ylab="An", xlim=(0,100), ylim=(-10,60), pdfname="BB-RH-An-CO2")
visualize_model_MED(group=:Weather=>:CO2=>[1500,800,400,300,200,100], xstep=rh_xstep,
x=:RH, y=:A_net, ylab="An", xlim=(0,100), ylim=(-10,60), pdfname="MED-RH-An-CO2")
# #### Stomatal Conductance
# ##### Ca
visualize_model_BB(group=rh_group,
x=:Ca, y=:gs, xlim=(0,1500), ylim=(0,0.8), pdfname="BB-Ca-gs-RH")
visualize_model_MED(group=rh_group,
x=:Ca, y=:gs, xlim=(0,1500), ylim=(0,0.8), pdfname="MED-Ca-gs-RH")
# ##### Ci
visualize_model_BB(group=rh_group,
legendpos=(0.8,0),
x=:Ci, y=:gs, xlim=(0,600), ylim=(0,0.8), pdfname="BB-Ci-gs-RH")
visualize_model_MED(group=rh_group,
legendpos=(0.8,0),
x=:Ci, y=:gs, xlim=(0,600), ylim=(0,0.8), pdfname="MED-Ci-gs-RH")
# ##### Ta
visualize_model_BB(group=rh_group, xstep=ta_xstep,
x=:T_air, y=:gs, xlim=(0,50), ylim=(0,0.4), pdfname="BB-T-gs-RH")
visualize_model_MED(group=rh_group, xstep=ta_xstep,
x=:T_air, y=:gs, xlim=(0,50), ylim=(0,0.4), pdfname="MED-T-gs-RH")
# ##### RH
visualize_model_BB(group=:Weather=>:CO2=>[100,200,300,400,800,1500], xstep=rh_xstep,
x=:RH, y=:gs, xlim=(0,100), ylim=(0,1.5), pdfname="BB-RH-gs-CO2")
visualize_model_MED(group=:Weather=>:CO2=>[100,200,300,400,800,1500], xstep=rh_xstep,
x=:RH, y=:gs, xlim=(0,100), ylim=(0,1.5), pdfname="MED-RH-gs-CO2")
# #### Surface Humidity
visualize_model_BB(group=rh_group,
x=:Ca, y=:hs, xlim=(0,1500), ylim=(0,1), pdfname="BB-Ca-hs-RH")
visualize_model_MED(group=rh_group,
x=:Ca, y=:hs, xlim=(0,1500), ylim=(0,1), pdfname="MED-Ca-hs-RH")
# #### Leaf Temperature
visualize_model_BB(group=rh_group,
x=:Ca, y=:T, ylab="Tl", xlim=(0,1500), ylim=(31,36), pdfname="BB-Ca-Tl-RH")
visualize_model_MED(group=rh_group,
x=:Ca, y=:T, ylab="Tl", xlim=(0,1500), ylim=(31,36), pdfname="MED-Ca-Tl-RH")
# ## Stress Response
# ### Nitrogen Stress
nitrogen_group = :Nitrogen => :N => 2:-0.5:0.5
nitrogen_xstep = :Nitrogen => :N => 0.5:0.01:2.0;
# #### Relative Humidity
visualize_model_MED(group=rh_group, xstep=nitrogen_xstep,
x=:Np, y=:A_net, xlab="N", ylab="An", ylim=(-10,60), pdfname="MED-N-An-RH")
visualize_model_MED(group=nitrogen_group, xstep=rh_xstep, legend="N", names=:Np,
x=:RH, y=:A_net, ylab="An", xlim=(0,100), ylim=(-10,60), pdfname="MED-N-RH-An")
# #### CO2
visualize_model_MED(group=:Weather=>:CO2=>[800,400,300,200,100], xstep=nitrogen_xstep,
x=:Np, y=:A_net, xlab="N", ylab="An", legend="Ca", ylim=(-10,60), pdfname="MED-N-An-Ca")
visualize_model_MED(group=nitrogen_group, xstep=co2_xstep, legend="N", names=:Np,
x=:Ca, y=:A_net, ylab="An", xlim=(0,1500), ylim=(-10,60), pdfname="MED-N-Ca-An")
visualize_model_MED(group=nitrogen_group, xstep=co2_xstep, legend="N", names=:Np,
x=:Ci, y=:A_net, ylab="An", xlim=(0,800), ylim=(-10,60), pdfname="MED-N-Ci-An")
# #### Air Temperature
visualize_model_MED(group=:Weather=>:T_air=>40:-5:10, xstep=nitrogen_xstep,
x=:Np, y=:A_net, xlab="N", ylab="An", legend="Ta", ylim=(-10,60), pdfname="MED-N-An-Ta")
visualize_model_MED(group=nitrogen_group, xstep=ta_xstep,
legend="Np", legendpos=(0.1,-0.1), names=:Np,
x=:T_air, y=:A_net, xlab="Ta", ylab="An", xlim=(0,50), ylim=(-10,60), pdfname="MED-N-Ta-An")
visualize_model_BB(group=nitrogen_group, xstep=ta_xstep,
legend="Np", legendpos=(0.1,-0.1), names=:Np,
x=:T_air, y=:A_net, xlab="Ta", ylab="An", xlim=(0,50), ylim=(-10,60), pdfname="BB-N-Ta-An")
# #### Irradiance
visualize_model_MED(group=:Weather=>:PFD=>1800:-400:600, xstep=nitrogen_xstep,
legendpos=(0.1,0.25),
x=:Np, y=:A_net, xlab="Np", ylab="An", legend="I", ylim=(-10,60), pdfname="MED-N-An-I")
visualize_model_BB(group=:Weather=>:PFD=>1800:-400:600, xstep=nitrogen_xstep,
legendpos=(0.1,0.25),
x=:Np, y=:A_net, xlab="Np", ylab="An", legend="I", ylim=(-10,60), pdfname="BB-N-An-I")
visualize_model_MED(group=nitrogen_group, xstep=:Weather=>:PFD=>0:10:2000, legend="N", names=:Np,
x=:PFD, y=:A_net, xlab="I", ylab="An", xlim=(0,2000), ylim=(-10,60), pdfname="MED-N-I-An")
# ### Water Stress
water_group = :StomataTuzet => :WP_leaf => 0:-0.5:-2
water_xstep = :StomataTuzet => :WP_leaf => -2:0.02:0;
# #### Relative Humidity
visualize_model_MED(group=rh_group, xstep=water_xstep,
legendpos=(0.1,-0.1),
x=:WP_leaf, y=:A_net, xlab="Ψv", ylab="An", ylim=(-10,60), pdfname="MED-Ψ-An-RH")
visualize_model_BB(group=rh_group, xstep=water_xstep,
legendpos=(0.1,-0.1),
x=:WP_leaf, y=:A_net, xlab="Ψv", ylab="An", ylim=(-10,60), pdfname="BB-Ψ-An-RH")
visualize_model_MED(group=water_group, xstep=rh_xstep,
x=:RH, y=:A_net, ylab="An", legend="Ψv", xlim=(0,100), ylim=(-10,60), pdfname="MED-Ψ-RH-An")
# #### CO2
visualize_model_MED(group=:Weather=>:CO2=>[1500,800,400,300,200,100], xstep=water_xstep,
x=:WP_leaf, y=:A_net, xlab="Ψv", ylab="An", legend="Ca", ylim=(-10,60), pdfname="MED-Ψ-An-Ca")
visualize_model_MED(group=water_group, xstep=co2_xstep,
x=:Ca, y=:A_net, ylab="An", legend="Ψv", xlim=(0,1500), ylim=(-10,60), pdfname="MED-Ψ-Ca-An")
visualize_model_MED(group=water_group, xstep=co2_xstep,
x=:Ci, y=:A_net, ylab="An", legend="Ψv", xlim=(0,800), ylim=(-10,60), pdfname="MED-Ψ-Ci-An")
# #### Air Temperature
visualize_model_MED(group=:Weather=>:T_air=>40:-5:10, xstep=water_xstep,
x=:WP_leaf, y=:A_net, xlab="Ψv", ylab="An", legend="Ta", ylim=(-10,60), pdfname="MED-Ψ-An-Ta")
visualize_model_MED(group=water_group, xstep=ta_xstep,
legendpos=(0.1,-0.1),
x=:T_air, y=:A_net, xlab="Ta", ylab="An", legend="Ψv", xlim=(0,50), ylim=(-10,60), pdfname="MED-Ψ-Ta-An")
visualize_model_BB(group=water_group, xstep=ta_xstep,
legendpos=(0.1,-0.1),
x=:T_air, y=:A_net, xlab="Ta", ylab="An", legend="Ψv", xlim=(0,50), ylim=(-10,60), pdfname="BB-Ψ-Ta-An")
# #### Irradiance
visualize_model_MED(group=:Weather=>:PFD=>1800:-400:200, xstep=water_xstep,
x=:WP_leaf, y=:A_net, xlab="Ψv", ylab="An", legend="I", ylim=(-10,60), pdfname="MED-Ψ-An-I")
visualize_model_MED(group=water_group, xstep=:Weather=>:PFD=>0:10:2000,
x=:PFD, y=:A_net, xlab="I", ylab="An", legend="Ψv", xlim=(0,2000), ylim=(-10,60), pdfname="MED-Ψ-I-An")
# ## Stress Interaction
visualize_stress(S::Type{<:GasExchange};
config=(),
configΔ=(),
x=:Np,
y=:WP_leaf,
z=:A_net,
xstep=:Nitrogen=>:N=>1:0.02:2,
ystep=:StomataTuzet=>:WP_leaf=>-2:0.04:0,
kind=:contour, #:heatmap,
legend=false,
aspect=1,
pdfname=nothing,
kwargs...
) = begin
p = visualize(S, x, y, z; config=(config, configΔ), kind, xstep, ystep, legend, aspect, kwargs...)
!isnothing(pdfname) && p' |> Gadfly.PDF("$pdfname.pdf", 10*Gadfly.cm)
p' |> Gadfly.SVG()
end
visualize_stress_BB(; config=bb_config, kw...) = visualize_stress(GasExchangeBallBerry; config=config, kw...)
visualize_stress_MED(; config=med_config, kw...) = visualize_stress(GasExchangeMedlyn; config=config, kw...)
visualize_stress(; kw...) = visualize_stress_MED(; kw...)
# ### RH
for x in (30, 50, 70, 90)
visualize_stress_BB(
configΔ=:Weather=>:RH=>x,
xlab="Np", ylab="Ψv", zlab="An", zlim=(-10,60), zgap=1, zlabgap=10,
pdfname="BB-NxΨ-RH-$x"
)
visualize_stress_MED(
configΔ=:Weather=>:RH=>x,
xlab="Np", ylab="Ψv", zlab="An", zlim=(-10,60), zgap=1, zlabgap=10,
pdfname="MED-NxΨ-RH-$x"
)
end
# ### CO2
for x in (200, 400, 600, 800)
visualize_stress_BB(
configΔ=:Weather=>:CO2=>x,