photosynthesis (version 1.0.2)

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)

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
$D_{c,0}$	D_c0	diffusion coefficient for CO2 in air at 0 <U+00B0>C	m${}^2$ / s	1.29e-5
$D_{h,0}$	D_h0	diffusion coefficient for heat in air at 0 <U+00B0>C	m${}^2$ / s	1.90e-5
$D_{m,0}$	D_m0	diffusion coefficient for momentum in air at 0 <U+00B0>C	m${}^2$ / s	1.33e-5
$D_{w,0}$	D_w0	diffusion coefficient for water vapor in air at 0 <U+00B0>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
$\sigma$	s	Stephan-Boltzmann constant	W / (m${}^2$ K${}^4$)	5.67e-08

Baking (i.e. temperature response) parameters:

Symbol	R	Description	Units	Default
$D_{\mathrm{s},\mathrm{gmc}}$	Ds_gmc	empirical temperature response parameter	J / (mol K)	487.29
$D_{\mathrm{s},\mathrm{Jmax}}$	Ds_Jmax	empirical temperature response parameter	J / (mol K)	388.04
$E_{\mathrm{a},\mathrm{\Gamma }\ast }$	Ea_gammastar	empirical temperature response parameter	J / mol	24459.97
$E_{\mathrm{a},\mathrm{gmc}}$	Ea_gmc	empirical temperature response parameter	J / mol	68901.56
$E_{\mathrm{a},\mathrm{Jmax}}$	Ea_Jmax	empirical temperature response parameter	J / mol	56095.18
$E_{\mathrm{a},\mathrm{KC}}$	Ea_KC	empirical temperature response parameter	J / mol	80989.78
$E_{\mathrm{a},\mathrm{KO}}$	Ea_KO	empirical temperature response parameter	J / mol	23719.97
$E_{\mathrm{a},\mathrm{Rd}}$	Ea_Rd	empirical temperature response parameter	J / mol	40446.75
$E_{\mathrm{a},\mathrm{Vcmax}}$	Ea_Vcmax	empirical temperature response parameter	J / mol	52245.78
$E_{\mathrm{d},\mathrm{gmc}}$	Ed_gmc	empirical temperature response parameter	J / mol	148788.56

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

Leaf parameters:

Symbol	R	Description	Units	Default
$d$	leafsize	leaf characteristic dimension	m	0.1
$\mathrm{\Gamma }\ast$	gamma_star	chloroplastic CO2 compensation point (T_leaf)	Pa	calculated
$\mathrm{\Gamma }{\ast }_{25}$	gamma_star25	chloroplastic CO2 compensation point (25 <U+00B0>C)	Pa	3.743
$g_{\mathrm{mc}}$	g_mc	mesophyll conductance to CO2 (T_leaf)	$\mu$mol CO2 / (m${}^2$ s Pa)	calculated
$g_{\mathrm{mc}}$	g_mc25	mesophyll conductance to CO2 (25 <U+00B0>C)	$\mu$mol CO2 / (m${}^2$ s Pa)	4
$g_{\mathrm{sc}}$	g_sc	stomatal conductance to CO2	$\mu$mol CO2 / (m${}^2$ s Pa)	4
$g_{\mathrm{uc}}$	g_uc	cuticular conductance to CO2	$\mu$mol CO2 / (m${}^2$ s Pa)	0.1
$J_{\max 25}$	J_max25	potential electron transport (25 <U+00B0>C)	$\mu$mol CO2 / (m${}^2$ s)	200
$J_{\max }$	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
$K_{\mathrm{C}25}$	K_C25	Michaelis constant for carboxylation (25 <U+00B0>C)	$\mu$mol / mol	268.3
$K_{\mathrm{C}}$	K_C	Michaelis constant for carboxylation (T_leaf)	$\mu$mol / mol	calculated
$K_{\mathrm{O}25}$	K_O25	Michaelis constant for oxygenation (25 <U+00B0>C)	$\mu$mol / mol	165084.2
$K_{\mathrm{O}}$	K_O	Michaelis constant for oxygenation (T_leaf)	$\mu$mol / mol	calculated
${\varphi }_J$	phi_J	initial slope of the response of J to PPFD	none	0.331
$R_{\mathrm{d}25}$	R_d25	nonphotorespiratory CO2 release (25 <U+00B0>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
$V_{\mathrm{c},\max 25}$	V_cmax25	maximum rate of carboxylation (25 <U+00B0>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
$V_{\mathrm{tpu}25}$	V_tpu25	rate of triose phosphate utilization (25 <U+00B0>C)	$\mu$mol CO2 / (m${}^2$ s)	200

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${}^2$	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 H2O) / (m${}^2$ s Pa)	converted from $g_{\mathrm{sc}}$
$g_{\mathrm{uw}}$	g_uw	cuticular conductance to H2O	($\mu$mol H2O) / (m${}^2$ s Pa)	converted from $g_{\mathrm{uc}}$

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

# NOT RUN {
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
)

# }