make_parameters: Make lists of parameters for 'optimize_leaf'

In cdmuir/leafoptimizer: Optimize leaf traits to different environments in silico

Description

Make lists of parameters for optimize_leaf

make_leafpar

make_enviropar

make_bakepar

make_constants

Usage

make_leafpar(replace = NULL)

make_enviropar(replace = NULL)

make_bakepar(replace = NULL)

make_constants(replace = NULL)

Arguments

replace

A named list of parameters to replace defaults. If NULL, defaults will be used.

Details

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	phi	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 utilisation (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

Environment parameters:

Symbol	R	Description	Units	Default
C_air	C_air	atmospheric CO2 concentration	Pa	41
E_q	E_q	energy per mole quanta	kJ / mol^2	220
f_PAR	f_par	fraction of S_sw that is photosynthetically active radiation (PAR)	none	0.5
O	O	atmospheric O2 concentration	kPa	21.27565
P	P	atmospheric pressure	kPa	101.3246
PPFD	PPFD	photosynthetic photon flux density	μmol quanta / (m^2 s)	1500
RH	RH	relative humidity	none	0.50
T_air	T_air	air temperature	K	298.15
u	wind	windspeed	m / s	2

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

Constants:

Symbol	R	Description	Units	Default
D_c0	D_c0	diffusion coefficient for CO2 in air at 0 °C	m^2 / s	12.9
D_h0	D_h0	diffusion coefficient for heat in air at 0 °C	m^2 / s	1.9e-5
D_m0	D_m0	diffusion coefficient for momentum in air at 0 °C	m^2 / s	13.3e-06
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

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

library(leafoptimizer)

bake_par <- make_bakepar()
constants <- make_constants()
enviro_par <- make_enviropar()
leaf_par <- make_leafpar()

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")
  )
)

cdmuir/leafoptimizer documentation built on Sept. 10, 2021, 7:28 p.m.