Make lists of parameters for photosynthesis
Make lists of parameters for photosynthesis
make_leafpar
make_enviropar
make_bakepar
make_constants
make_leafpar(replace = NULL, use_tealeaves) make_enviropar(replace = NULL, use_tealeaves) make_bakepar(replace = NULL) make_constants(replace = NULL, use_tealeaves)
replace |
A named list of parameters to replace defaults.
If |
use_tealeaves |
Logical. Should leaf energy balance be used to calculate leaf temperature (T_leaf)? If TRUE, |
Constants:
| Symbol | R | Description | Units | Default |
| D_c0 | D_c0 |
diffusion coefficient for CO2 in air at 0 °C | m^2 / s | 1.29e-5 |
| D_h0 | D_h0 |
diffusion coefficient for heat in air at 0 °C | m^2 / s | 1.90e-5 |
| D_m0 | D_m0 |
diffusion coefficient for momentum in air at 0 °C | m^2 / s | 1.33e-5 |
| D_w0 | D_w0 |
diffusion coefficient for water vapor in air at 0 °C | m^2 / s | 2.12e-5 |
| ε | 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) | 8.3144598 |
| σ | s |
Stephan-Boltzmann constant | W / (m^2 K^4) | 5.67e-08 |
| Sh | Sh |
Sherwood number | none | calculated |
Baking (i.e. temperature response) parameters:
| Symbol | R | Description | Units | Default |
| Ds_gmc | Ds_gmc |
empirical temperature response parameter | J / (mol K) | 487.29 |
| Ds_Jmax | Ds_Jmax |
empirical temperature response parameter | J / (mol K) | 388.04 |
| Ea_gammastar | Ea_gammastar |
empirical temperature response parameter | J / mol | 24459.97 |
| Ea_gmc | Ea_gmc |
empirical temperature response parameter | J / mol | 68901.56 |
| Ea_Jmax | Ea_Jmax |
empirical temperature response parameter | J / mol | 56095.18 |
| Ea_KC | Ea_KC |
empirical temperature response parameter | J / mol | 80989.78 |
| Ea_KO | Ea_KO |
empirical temperature response parameter | J / mol | 23719.97 |
| Ea_Rd | Ea_Rd |
empirical temperature response parameter | J / mol | 40446.75 |
| Ea_Vcmax | Ea_Vcmax |
empirical temperature response parameter | J / mol | 52245.78 |
| Ed_gmc | Ed_gmc |
empirical temperature response parameter | J / mol | 148788.56 |
| Ed_Jmax | Ed_Jmax |
empirical temperature response parameter | J / mol | 121244.79 |
Environment parameters:
| Symbol | R | Description | Units | Default |
| C_air | C_air |
atmospheric CO2 concentration | Pa | 41 |
| O | O |
atmospheric O2 concentration | kPa | 21.27565 |
| P | P |
atmospheric pressure | kPa | 101.3246 |
| PPFD | PPFD |
photosynthetic photon flux density | umol quanta / (m^2 s) | 1500 |
| RH | RH |
relative humidity | none | 0.50 |
| u | wind |
windspeed | m / s | 2 |
Leaf parameters:
| Symbol | R | Description | Units | Default |
| d | leafsize |
leaf characteristic dimension | m | 0.1 |
| Γ* | gamma_star |
chloroplastic CO2 compensation point (T_leaf) | Pa | calculated |
| Γ_25* | gamma_star25 |
chloroplastic CO2 compensation point (25 °C) | Pa | 3.743 |
| g_mc | g_mc |
mesophyll conductance to CO2 (T_leaf) | μmol CO2 / (m^2 s Pa) | calculated |
| g_mc | g_mc25 |
mesophyll conductance to CO2 (25 °C) | μmol CO2 / (m^2 s Pa) | 4 |
| g_sc | g_sc |
stomatal conductance to CO2 | μmol CO2 / (m^2 s Pa) | 4 |
| g_uc | g_uc |
cuticular conductance to CO2 | μmol CO2 / (m^2 s Pa) | 0.1 |
| J_max25 | J_max25 |
potential electron transport (25 °C) | μmol CO2 / (m^2 s) | 200 |
| J_max | J_max |
potential electron transport (T_leaf) | μmol CO2 / (m^2 s) | calculated |
| k_mc | k_mc |
partition of g_mc to lower mesophyll | none | 1 |
| k_sc | k_sc |
partition of g_sc to lower surface | none | 1 |
| k_uc | k_uc |
partition of g_uc to lower surface | none | 1 |
| K_C25 | K_C25 |
Michaelis constant for carboxylation (25 °C) | μmol / mol | 268.3 |
| K_C | K_C |
Michaelis constant for carboxylation (T_leaf) | μmol / mol | calculated |
| K_O25 | K_O25 |
Michaelis constant for oxygenation (25 °C) | μmol / mol | 165084.2 |
| K_O | K_O |
Michaelis constant for oxygenation (T_leaf) | μmol / mol | calculated |
| φ_J | phi_J |
initial slope of the response of J to PPFD | none | 0.331 |
| R_d25 | R_d25 |
nonphotorespiratory CO2 release (25 °C) | μmol CO2 / (m^2 s) | 2 |
| R_d | R_d |
nonphotorespiratory CO2 release (T_leaf) | μmol CO2 / (m^2 s) | calculated |
| θ_J | theta_J |
curvature factor for light-response curve | none | 0.825 |
| T_leaf | T_leaf |
leaf temperature | K | 298.15 |
| V_c,max25 | V_cmax25 |
maximum rate of carboxylation (25 °C) | μmol CO2 / (m^2 s) | 150 |
| V_c,max | V_cmax |
maximum rate of carboxylation (T_leaf) | μmol CO2 / (m^2 s) | calculated |
| V_tpu25 | V_tpu25 |
rate of triose phosphate utilization (25 °C) | μmol CO2 / (m^2 s) | 200 |
| V_tpu | V_tpu |
rate of triose phosphate utilisation (T_leaf) | μmol CO2 / (m^2 s) | calculated |
If use_tealeaves = TRUE, additional parameters are:
Constants:
| Symbol | R | Description | Units | Default |
| c_p | c_p |
heat capacity of air | J / (g K) | 1.01 |
| R_air | R_air |
specific gas constant for dry air | J / (kg K) | 287.058 |
Environmental parameters:
| Symbol | R | Description | Units | Default |
| E_q | E_q |
energy per mole quanta | kJ / mol^2 | 220 |
| f_PAR | f_par |
fraction of incoming shortwave radiation that is photosynthetically active radiation (PAR) | none | 0.5 |
| r | r |
reflectance for shortwave irradiance (albedo) | none | 0.2 |
| T_air | T_air |
air temperature | K | 298.15 |
Leaf parameters:
| Symbol | R | Description | Units | Default |
| α_l | abs_l |
absorbtivity of longwave radiation (4 - 80 μm) | none | 0.97 |
| α_s | abs_s |
absorbtivity of shortwave radiation (0.3 - 4 μm) | none | 0.50 |
| g_sw | g_sw |
stomatal conductance to H2O | (μmol H2O) / (m^2 s Pa) | converted from g_sc |
| g_uw | g_uw |
cuticular conductance to H2O | (μmol H2O) / (m^2 s Pa) | converted from g_uc |
| logit(sr) | logit_sr |
stomatal ratio (logit transformed) | none | converted from k_sc |
make_leafpar: An object inheriting from class leaf_parmake_enviropar: An object inheriting from class enviro_parmake_bakepar: An object inheriting from class bake_parmake_constants: An object inheriting from class constants
Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.
bake_par <- make_bakepar()
constants <- make_constants(use_tealeaves = FALSE)
enviro_par <- make_enviropar(use_tealeaves = FALSE)
leaf_par <- make_leafpar(use_tealeaves = FALSE)
leaf_par <- make_leafpar(
replace = list(
g_sc = set_units(3, "umol/m^2/s/Pa"),
V_cmax25 = set_units(100, "umol/m^2/s")
), use_tealeaves = FALSE
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