| photosynthesis {photosynthesis} | R Documentation |
Simulate C3 photosynthesis
Description
photosynthesis: simulate C3 photosynthesis over multiple parameter sets
photo: simulate C3 photosynthesis over a single parameter set
Usage
photosynthesis(
leaf_par,
enviro_par,
bake_par,
constants,
use_tealeaves,
progress = TRUE,
quiet = FALSE,
assert_units = TRUE,
check = TRUE,
parallel = FALSE,
use_legacy_version = FALSE
)
photo(
leaf_par,
enviro_par,
bake_par,
constants,
use_tealeaves,
quiet = FALSE,
assert_units = TRUE,
check = TRUE,
prepare_for_tleaf = use_tealeaves,
use_legacy_version = FALSE
)
Arguments
leaf_par |
A list of leaf parameters inheriting class |
enviro_par |
A list of environmental parameters inheriting class |
bake_par |
A list of temperature response parameters inheriting class |
constants |
A list of physical constants inheriting class |
use_tealeaves |
Logical. Should leaf energy balance be used to calculate leaf temperature (T_leaf)? If TRUE, |
progress |
Logical. Should a progress bar be displayed? |
quiet |
Logical. Should messages be displayed? |
assert_units |
Logical. Should parameter |
check |
Logical. Should arguments checks be done? This is intended to be disabled when |
parallel |
Logical. Should parallel processing be used via |
use_legacy_version |
Logical. Should legacy model (<2.1.0) be used? See NEWS for further information. Default is FALSE. |
prepare_for_tleaf |
Logical. Should arguments additional calculations for |
Details
photo: This function takes simulates photosynthetic rate using the Farquhar-von Caemmerer-Berry (FvCB()) model of C3 photosynthesis for single combined set of leaf parameters (leaf_par()), environmental parameters (enviro_par()), and physical constants (constants()). Leaf parameters are provided at reference temperature (25 °C) and then "baked" to the appropriate leaf temperature using temperature response functions (see bake()).
photosynthesis: This function uses photo to simulate photosynthesis over multiple parameter sets that are generated using cross_df().
Value
A data.frame with the following units columns
Inputs:
| Symbol | R | Description | Units | Default |
D_{\mathrm{c},0} | D_c0 | diffusion coefficient for CO2 in air at 0 °C | m^2 / s | 1.29\times 10^{-5} |
D_{\mathrm{h},0} | D_h0 | diffusion coefficient for heat in air at 0 °C | m^2 / s | 1.90\times 10^{-5} |
D_{\mathrm{m},0} | D_m0 | diffusion coefficient for momentum in air at 0 °C | m^2 / s | 1.33\times 10^{-5} |
D_{\mathrm{w},0} | D_w0 | diffusion coefficient for water vapor in air at 0 °C | m^2 / s | 2.12\times 10^{-5} |
\epsilon | epsilon | ratio of water to air molar masses | none | 0.622 |
G | G | gravitational acceleration | m / s^2 | 9.8 |
eT | eT | exponent for temperature dependence of diffusion | none | 1.75 |
R | R | ideal gas constant | J / mol / K | 8.31 |
\sigma | sigma | Stephan-Boltzmann constant | W / m^2 / K^4 | 5.67\times 10^{-8} |
f_\mathrm{Sh} | f_sh | function to calculate constant(s) for Sherwood number | none | NA |
f_\mathrm{Nu} | f_nu | function to calculate constant(s) for Nusselt number | none | NA |
D_\mathrm{s,gmc} | Ds_gmc | empirical temperature response parameter | J / mol / K | 487 |
D_\mathrm{s,Jmax} | Ds_Jmax | empirical temperature response parameter | J / mol / K | 388 |
E_\mathrm{a,\Gamma *} | Ea_gammastar | empirical temperature response parameter | J / mol | 24500 |
E_\mathrm{a,gmc} | Ea_gmc | empirical temperature response parameter | J / mol | 68900 |
E_\mathrm{a,Jmax} | Ea_Jmax | empirical temperature response parameter | J / mol | 56100 |
E_\mathrm{a,KC} | Ea_KC | empirical temperature response parameter | J / mol | 81000 |
E_\mathrm{a,KO} | Ea_KO | empirical temperature response parameter | J / mol | 23700 |
E_\mathrm{a,Rd} | Ea_Rd | empirical temperature response parameter | J / mol | 40400 |
E_\mathrm{a,Vcmax} | Ea_Vcmax | empirical temperature response parameter | J / mol | 52200 |
E_\mathrm{a,Vtpu} | Ea_Vtpu | empirical temperature response parameter | J / mol | 52200 |
E_\mathrm{d,gmc} | Ed_gmc | empirical temperature response parameter | J / mol | 149000 |
E_\mathrm{d,Jmax} | Ed_Jmax | empirical temperature response parameter | J / mol | 121000 |
C_\mathrm{air} | C_air | atmospheric CO2 concentration | umol/mol | 420 |
O | O | atmospheric O2 concentration | mol/mol | 0.21 |
P | P | atmospheric pressure | kPa | 101 |
\mathrm{PPFD} | PPFD | photosynthetic photon flux density | umol / m^2 / s | 1500 |
\mathrm{RH} | RH | relative humidity | none | 0.5 |
u | wind | windspeed | m / s | 2 |
d | leafsize | leaf characteristic dimension | m | 0.1 |
\Gamma*_{25} | gamma_star25 | chloroplastic CO2 compensation point (25 °C) | umol/mol | 37.9 |
g_\mathrm{mc,25} | g_mc25 | mesophyll conductance to CO2 (25 °C) | mol / m^2 / s | 0.4 |
g_\mathrm{sc} | g_sc | stomatal conductance to CO2 | mol / m^2 / s | 0.4 |
g_\mathrm{uc} | g_uc | cuticular conductance to CO2 | mol / m^2 / s | 0.01 |
J_\mathrm{max,25} | J_max25 | potential electron transport (25 °C) | umol / m^2 / s | 200 |
k_\mathrm{mc} | k_mc | partition of g_mc to lower mesophyll | none | 1 |
k_\mathrm{sc} | k_sc | partition of g_sc to lower surface | none | 1 |
k_\mathrm{uc} | k_uc | partition of g_uc to lower surface | none | 1 |
K_\mathrm{C,25} | K_C25 | Michaelis constant for carboxylation (25 °C) | umol / mol | 268 |
K_\mathrm{O,25} | K_O25 | Michaelis constant for oxygenation (25 °C) | umol / mol | 165000 |
\phi_J | phi_J | initial slope of the response of J to PPFD | none | 0.331 |
R_\mathrm{d,25} | R_d25 | nonphotorespiratory CO2 release (25 °C) | umol / m^2 / s | 2 |
\theta_J | theta_J | curvature factor for light-response curve | none | 0.825 |
T_\mathrm{leaf} | T_leaf | leaf temperature | K | 298 |
V_\mathrm{c,max,25} | V_cmax25 | maximum rate of carboxylation (25 °C) | umol / m^2 / s | 150 |
V_\mathrm{tpu,25} | V_tpu25 | rate of triose phosphate utilization (25 °C) | umol / m^2 / s | 200 |
\delta_\mathrm{ias,lower} | delta_ias_lower | effective distance through lower internal airspace | um | NA |
\delta_\mathrm{ias,upper} | delta_ias_upper | effective distance through upper internal airspace | um | NA |
A_\mathrm{mes} / A | A_mes_A | mesophyll surface area per unit leaf area | none | NA |
g_\mathrm{liq,c,25} | g_liqc25 | liquid-phase conductance to CO2 (25 °C) | mol / m^2 / s | NA |
| Baked Inputs: | ||||
| Symbol | R | Description | Units | Default |
| :---------------------------- | :------------------- | :------------------------------------------------------------------- | :-------------------- | :------- |
\Gamma* | gamma_star | chloroplastic CO2 compensation point (T_leaf) | umol/mol | NA |
g_\mathrm{mc} | g_mc | mesophyll conductance to CO2 (T_leaf) | mol / m^2 / s | NA |
J_\mathrm{max} | J_max | potential electron transport (T_leaf) | umol / m^2 / s | NA |
K_\mathrm{C} | K_C | Michaelis constant for carboxylation (T_leaf) | umol / mol | NA |
K_\mathrm{O} | K_O | Michaelis constant for oxygenation (T_leaf) | umol / mol | NA |
R_\mathrm{d} | R_d | nonphotorespiratory CO2 release (T_leaf) | umol / m^2 / s | NA |
V_\mathrm{c,max} | V_cmax | maximum rate of carboxylation (T_leaf) | umol / m^2 / s | NA |
V_\mathrm{tpu} | V_tpu | rate of triose phosphate utilisation (T_leaf) | umol / m^2 / s | NA |
g_\mathrm{liq,c} | g_liqc | liquid-phase conductance to CO2 (T_leaf) | mol / m^2 / s | NA |
g_\mathrm{ias,c,lower} | g_iasc_lower | internal airspace conductance to CO2 in lower part of leaf (T_leaf) | mol / m^2 / s | NA |
g_\mathrm{ias,c,upper} | g_iasc_upper | internal airspace conductance to CO2 in upper part of leaf (T_leaf) | mol / m^2 / s | NA |
| Output: | |
A | photosynthetic rate at C_chl (\mumol CO2 / m^2 / s) |
C_chl | chloroplastic CO2 concentration where A_supply intersects A_demand (mumol / mol) |
C_i | intercellular CO2 concentration where A_supply intersects A_demand (mumol / mol) |
g_tc | total conductance to CO2 at T_leaf (mol / m^2 / s)) |
value | A_supply - A_demand (\mumol / (m^2 s)) at C_chl |
convergence | convergence code (0 = converged) |
Examples
# Single parameter set with 'photo'
bake_par = make_bakepar()
constants = make_constants(use_tealeaves = FALSE)
enviro_par = make_enviropar(use_tealeaves = FALSE)
leaf_par = make_leafpar(use_tealeaves = FALSE)
photo(leaf_par, enviro_par, bake_par, constants,
use_tealeaves = FALSE
)
# Multiple parameter sets with 'photosynthesis'
leaf_par = make_leafpar(
replace = list(
T_leaf = set_units(c(293.14, 298.15), "K")
), use_tealeaves = FALSE
)
photosynthesis(leaf_par, enviro_par, bake_par, constants,
use_tealeaves = FALSE
)