photosynthesis (version 2.0.3)

make_parameters: 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)

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

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
\(D_{c,0}\)	D_c0	diffusion coefficient for CO2 in air at 0 °C	m\(^2\) / s	1.29e-5
\(D_{h,0}\)	D_h0	diffusion coefficient for heat in air at 0 °C	m\(^2\) / s	1.90e-5
\(D_{m,0}\)	D_m0	diffusion coefficient for momentum in air at 0 °C	m\(^2\) / s	1.33e-5
\(D_{w,0}\)	D_w0	diffusion coefficient for water vapor in air at 0 °C	m\(^2\) / s	2.12e-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)	8.3144598
\(\sigma\)	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
\(D_\mathrm{s,gmc}\)	Ds_gmc	empirical temperature response parameter	J / (mol K)	487.29
\(D_\mathrm{s,Jmax}\)	Ds_Jmax	empirical temperature response parameter	J / (mol K)	388.04
\(E_\mathrm{a,\Gamma *}\)	Ea_gammastar	empirical temperature response parameter	J / mol	24459.97
\(E_\mathrm{a,gmc}\)	Ea_gmc	empirical temperature response parameter	J / mol	68901.56
\(E_\mathrm{a,Jmax}\)	Ea_Jmax	empirical temperature response parameter	J / mol	56095.18
\(E_\mathrm{a,KC}\)	Ea_KC	empirical temperature response parameter	J / mol	80989.78
\(E_\mathrm{a,KO}\)	Ea_KO	empirical temperature response parameter	J / mol	23719.97
\(E_\mathrm{a,Rd}\)	Ea_Rd	empirical temperature response parameter	J / mol	40446.75
\(E_\mathrm{a,Vcmax}\)	Ea_Vcmax	empirical temperature response parameter	J / mol	52245.78
\(E_\mathrm{d,gmc}\)	Ed_gmc	empirical temperature response parameter	J / mol	148788.56
\(E_\mathrm{d,Jmax}\)	Ed_Jmax	empirical temperature response parameter	J / mol	121244.79

Environment parameters:

Symbol	R	Description	Units	Default
\(C_\mathrm{air}\)	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
\(\mathrm{RH}\)	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
\(\Gamma*\)	gamma_star	chloroplastic CO2 compensation point (T_leaf)	Pa	calculated
\(\Gamma*_{25}\)	gamma_star25	chloroplastic CO2 compensation point (25 °C)	Pa	3.743
\(g_\mathrm{mc}\)	g_mc	mesophyll conductance to CO2 (T_leaf)	\(\mu\)mol / (m\(^2\) s Pa)	calculated
\(g_\mathrm{mc}\)	g_mc25	mesophyll conductance to CO2 (25 °C)	\(\mu\)mol / (m\(^2\) s Pa)	4
\(g_\mathrm{sc}\)	g_sc	stomatal conductance to CO2	\(\mu\)mol / (m\(^2\) s Pa)	4
\(g_\mathrm{uc}\)	g_uc	cuticular conductance to CO2	\(\mu\)mol / (m\(^2\) s Pa)	0.1
\(J_\mathrm{max25}\)	J_max25	potential electron transport (25 °C)	\(\mu\)mol CO2 / (m\(^2\) s)	200
\(J_\mathrm{max}\)	J_max	potential electron transport (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(k_\mathrm{mc}\)	k_mc	partition of \(g_\mathrm{mc}\) to lower mesophyll	none	1
\(k_\mathrm{sc}\)	k_sc	partition of \(g_\mathrm{sc}\) to lower surface	none	1
\(k_\mathrm{uc}\)	k_uc	partition of \(g_\mathrm{uc}\) to lower surface	none	1
\(K_\mathrm{C25}\)	K_C25	Michaelis constant for carboxylation (25 °C)	\(\mu\)mol / mol	268.3
\(K_\mathrm{C}\)	K_C	Michaelis constant for carboxylation (T_leaf)	\(\mu\)mol / mol	calculated
\(K_\mathrm{O25}\)	K_O25	Michaelis constant for oxygenation (25 °C)	\(\mu\)mol / mol	165084.2
\(K_\mathrm{O}\)	K_O	Michaelis constant for oxygenation (T_leaf)	\(\mu\)mol / mol	calculated
\(\phi_J\)	phi_J	initial slope of the response of J to PPFD	none	0.331
\(R_\mathrm{d25}\)	R_d25	nonphotorespiratory CO2 release (25 °C)	\(\mu\)mol CO2 / (m\(^2\) s)	2
\(R_\mathrm{d}\)	R_d	nonphotorespiratory CO2 release (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(\theta_J\)	theta_J	curvature factor for light-response curve	none	0.825
\(T_\mathrm{leaf}\)	T_leaf	leaf temperature	K	298.15
\(V_\mathrm{c,max25}\)	V_cmax25	maximum rate of carboxylation (25 °C)	\(\mu\)mol CO2 / (m\(^2\) s)	150
\(V_\mathrm{c,max}\)	V_cmax	maximum rate of carboxylation (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(V_\mathrm{tpu25}\)	V_tpu25	rate of triose phosphate utilization (25 °C)	\(\mu\)mol CO2 / (m\(^2\) s)	200
\(V_\mathrm{tpu}\)	V_tpu	rate of triose phosphate utilisation (T_leaf)	\(\mu\)mol 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
\(R_\mathrm{air}\)	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	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	298.15

Leaf parameters:

Symbol	R	Description	Units	Default
\(\alpha_\mathrm{l}\)	abs_l	absorbtivity of longwave radiation (4 - 80 \(\mu\)m)	none	0.97
\(\alpha_\mathrm{s}\)	abs_s	absorbtivity of shortwave radiation (0.3 - 4 \(\mu\)m)	none	0.50
\(g_\mathrm{sw}\)	g_sw	stomatal conductance to H2O	(\(\mu\)mol) / (m\(^2\) s Pa)	converted from \(g_\mathrm{sc}\)
\(g_\mathrm{uw}\)	g_uw	cuticular conductance to H2O	(\(\mu\)mol) / (m\(^2\) s Pa)	converted from \(g_\mathrm{uc}\)
\(\mathrm{logit}(sr)\)	logit_sr	stomatal ratio (logit transformed)	none	converted from \(k_\mathrm{sc}\)

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(3, "umol/m^2/s/Pa"),
    V_cmax25 = set_units(100, "umol/m^2/s")
  ), use_tealeaves = FALSE
)