make_parameters: Make lists of parameters for 'photosynthesis'
In photosynthesis: Tools for Plant Ecophysiology & Modeling
make_parameters R Documentation
Make lists of parameters for photosynthesis
Description
Make lists of parameters for photosynthesis
make_leafpar
make_enviropar
make_bakepar
make_constants
Usage
make_leafpar(replace = NULL, use_tealeaves)
make_enviropar(replace = NULL, use_tealeaves)
make_bakepar(replace = NULL)
make_constants(replace = NULL, use_tealeaves)
Arguments
replace
A named list of parameters to replace defaults.
If NULL, defaults will be used.
use_tealeaves
Logical. Should leaf energy balance be used to calculate leaf temperature (T_leaf)? If TRUE, tleaf() calculates T_leaf. If FALSE, user-defined T_leaf is used. Additional parameters and constants are required, see make_parameters().
Details
Constants:
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
Baking (i.e. temperature response) parameters:
Symbol R Description Units Default
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
Environment parameters:
Symbol R Description Units Default
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
Leaf parameters:
Symbol R Description Units Default
d leafsize leaf characteristic dimension m 0.1
\Gamma* gamma_star chloroplastic CO2 compensation point (T_leaf) umol/mol NA
\Gamma*_{25} gamma_star25 chloroplastic CO2 compensation point (25 °C) umol/mol 37.9
g_\mathrm{mc} g_mc mesophyll conductance to CO2 (T_leaf) mol / m^2 / s NA
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
J_\mathrm{max} J_max potential electron transport (T_leaf) umol / m^2 / s NA
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{C} K_C Michaelis constant for carboxylation (T_leaf) umol / mol NA
K_\mathrm{O,25} K_O25 Michaelis constant for oxygenation (25 °C) umol / mol 165000
K_\mathrm{O} K_O Michaelis constant for oxygenation (T_leaf) umol / mol NA
\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
R_\mathrm{d} R_d nonphotorespiratory CO2 release (T_leaf) umol / m^2 / s NA
\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{c,max} V_cmax maximum rate of carboxylation (T_leaf) umol / m^2 / s NA
V_\mathrm{tpu,25} V_tpu25 rate of triose phosphate utilization (25 °C) umol / m^2 / s 200
V_\mathrm{tpu} V_tpu rate of triose phosphate utilisation (T_leaf) umol / m^2 / s NA
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_\mathrm{air} R_air specific gas constant for dry air J / kg / K 287
Baking (i.e. temperature response) parameters:
Symbol R Description Units Default
Environment parameters:
Symbol R Description Units Default
E_q E_q energy per mole quanta kJ / mol 220
f_\mathrm{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_\mathrm{air} T_air air temperature K 298
T_\mathrm{sky} T_sky sky temperature K NA
Leaf parameters:
Symbol R Description Units Default
\alpha_\mathrm{l} abs_l absorbtivity of longwave radiation (4 - 80 um) none 0.97
\alpha_\mathrm{s} abs_s absorbtivity of shortwave radiation (0.3 - 4 um) none 0.5
g_\mathrm{sw} g_sw stomatal conductance to H2O mol / m^2 / s NA
g_\mathrm{uw} g_uw cuticular conductance to H2O mol / m^2 / s NA
\mathrm{logit}(sr) logit_sr stomatal ratio (logit transformed) none NA
Optional leaf parameters:
Symbol R Description Units Default
\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
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
Value
make_leafpar: An object inheriting from class leaf_par()
make_enviropar: An object inheriting from class enviro_par()
make_bakepar: An object inheriting from class bake_par()
make_constants: An object inheriting from class constants()
References
Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic
rate into contributions from different variables. Plant, Cell & Environment
38: 1200-11.
Examples
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(0.3, mol / m^2 / s),
V_cmax25 = set_units(100, umol / m^2 / s)
), use_tealeaves = FALSE
)
photosynthesis documentation built on Aug. 15, 2023, 9:08 a.m.
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| make_parameters | R Documentation |
Make lists of parameters for photosynthesis
Description
Make lists of parameters for photosynthesis
make_leafpar
make_enviropar
make_bakepar
make_constants
Usage
make_leafpar(replace = NULL, use_tealeaves)
make_enviropar(replace = NULL, use_tealeaves)
make_bakepar(replace = NULL)
make_constants(replace = NULL, use_tealeaves)
Arguments
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, |
Details
Constants:
| 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 |
Baking (i.e. temperature response) parameters:
| Symbol | R | Description | Units | Default |
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 |
Environment parameters:
| Symbol | R | Description | Units | Default |
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 |
Leaf parameters:
| Symbol | R | Description | Units | Default |
d | leafsize | leaf characteristic dimension | m | 0.1 |
\Gamma* | gamma_star | chloroplastic CO2 compensation point (T_leaf) | umol/mol | NA |
\Gamma*_{25} | gamma_star25 | chloroplastic CO2 compensation point (25 °C) | umol/mol | 37.9 |
g_\mathrm{mc} | g_mc | mesophyll conductance to CO2 (T_leaf) | mol / m^2 / s | NA |
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 |
J_\mathrm{max} | J_max | potential electron transport (T_leaf) | umol / m^2 / s | NA |
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{C} | K_C | Michaelis constant for carboxylation (T_leaf) | umol / mol | NA |
K_\mathrm{O,25} | K_O25 | Michaelis constant for oxygenation (25 °C) | umol / mol | 165000 |
K_\mathrm{O} | K_O | Michaelis constant for oxygenation (T_leaf) | umol / mol | NA |
\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 |
R_\mathrm{d} | R_d | nonphotorespiratory CO2 release (T_leaf) | umol / m^2 / s | NA |
\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{c,max} | V_cmax | maximum rate of carboxylation (T_leaf) | umol / m^2 / s | NA |
V_\mathrm{tpu,25} | V_tpu25 | rate of triose phosphate utilization (25 °C) | umol / m^2 / s | 200 |
V_\mathrm{tpu} | V_tpu | rate of triose phosphate utilisation (T_leaf) | umol / m^2 / s | NA |
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_\mathrm{air} | R_air | specific gas constant for dry air | J / kg / K | 287 |
Baking (i.e. temperature response) parameters:
| Symbol | R | Description | Units | Default |
Environment parameters:
| Symbol | R | Description | Units | Default |
E_q | E_q | energy per mole quanta | kJ / mol | 220 |
f_\mathrm{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_\mathrm{air} | T_air | air temperature | K | 298 |
T_\mathrm{sky} | T_sky | sky temperature | K | NA |
Leaf parameters:
| Symbol | R | Description | Units | Default |
\alpha_\mathrm{l} | abs_l | absorbtivity of longwave radiation (4 - 80 um) | none | 0.97 |
\alpha_\mathrm{s} | abs_s | absorbtivity of shortwave radiation (0.3 - 4 um) | none | 0.5 |
g_\mathrm{sw} | g_sw | stomatal conductance to H2O | mol / m^2 / s | NA |
g_\mathrm{uw} | g_uw | cuticular conductance to H2O | mol / m^2 / s | NA |
\mathrm{logit}(sr) | logit_sr | stomatal ratio (logit transformed) | none | NA |
Optional leaf parameters:
| Symbol | R | Description | Units | Default |
\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 |
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 |
Value
make_leafpar: An object inheriting from class leaf_par()
make_enviropar: An object inheriting from class enviro_par()
make_bakepar: An object inheriting from class bake_par()
make_constants: An object inheriting from class constants()
References
Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.
Examples
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(0.3, mol / m^2 / s),
V_cmax25 = set_units(100, umol / m^2 / s)
), use_tealeaves = FALSE
)
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