Make lists of parameters for photosynthesis — make

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().

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()

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

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

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
)