FvCB

W_carbox

W_regen

W_tpu

Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
Rubisco-limited assimilation rate
RuBP regeneration-limited assimilation rate
TPU-limited assimilation rate

Contains modeling and analytical tools for plant ecophysiology.
MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer,
Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and
Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that
parameters are properly specified and transformed before calculations.
Temperature response functions get automatically "baked" into all
parameters based on leaf temperature following Bernacchi et al. (2002)
<doi:10.1104/pp.008250>. The package includes boundary layer, cuticular,
stomatal, and mesophyll conductances to CO2, which each can vary on the
upper and lower portions of the leaf. Use straightforward functions to
simulate photosynthesis over environmental gradients such as Photosynthetic
Photon Flux Density (PPFD) and leaf temperature, or over trait gradients
such as CO2 conductance or photochemistry.
ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>)
and AQ curves (Marshall & Biscoe (1980) <doi:10.1093/jxb/31.1.29>),
temperature responses (Heskel et al. (2016) <doi:10.1073/pnas.1520282113>;
Kruse et al. (2008) <doi:10.1111/j.1365-3040.2008.01809.x>, Medlyn et al.
(2002) <doi:10.1046/j.1365-3040.2002.00891.x>, Hobbs et al. (2013)
<doi:10.1021/cb4005029>), respiration in the light (Kok (1956)
<doi:10.1016/0006-3002(56)90003-8>, Walker & Ort (2015) <doi:10.1111/pce.12562>,
Yin et al. (2009) <doi:10.1111/j.1365-3040.2009.01934.x>, Yin et al. (2011)
<doi:10.1093/jxb/err038>), mesophyll conductance (Harley et al. (1992)
<doi:10.1104/pp.98.4.1429>), pressure-volume curves (Koide et al. (2000)
<doi:10.1007/978-94-009-2221-1_9>, Sack et al. (2003)
<doi:10.1046/j.0016-8025.2003.01058.x>, Tyree et al. (1972)
<doi:10.1093/jxb/23.1.267>), hydraulic vulnerability curves (Ogle et al. (2009)
<doi:10.1111/j.1469-8137.2008.02760.x>, Pammenter et al. (1998)
<doi:10.1093/treephys/18.8-9.589>), and tools for running sensitivity
analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(),
R_d()).

Chris Muir

photosynthesis

Tools for Plant Ecophysiology & Modeling

Joseph Stinziano

Cassaundra Roback

Demi Sargent

Bridget Murphy

Patrick Hudson

FvCB function

<dl><dt>C_chl</dt>
<dd>Chloroplastic CO2 concentration in Pa of class <code>units</code></dd>
<dt>pars</dt>
<dd>Concatenated parameters (<code>leaf_par</code>, <code>enviro_par</code>, and <code>constants</code>)</dd>
<dt>unitless</dt>
<dd>Logical. Should <code>units</code> be set? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.</dd></dl>

Arguments

Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model — FvCB

<dl>

<dt>C_chl</dt>
<dd>Chloroplastic CO2 concentration in Pa of class <code>units</code></dd>


<dt>pars</dt>
<dd>Concatenated parameters (<code>leaf_par</code>, <code>enviro_par</code>, and <code>constants</code>)</dd>


<dt>unitless</dt>
<dd>Logical. Should <code>units</code> be set? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.</dd>

</dl>

Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model

Symbol	R	Description	Units	Default
\(C_\mathrm{chl}\)	`C_chl`	chloroplastic CO2 concentration	Pa	input
\(\Gamma*\)	`gamma_star`	chloroplastic CO2 compensation point (T_leaf)	Pa	calculated
\(J_\mathrm{max}\)	`J_max`	potential electron transport (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(K_\mathrm{C}\)	`K_C`	Michaelis constant for carboxylation (T_leaf)	\(\mu\)mol / mol	calculated
\(K_\mathrm{O}\)	`K_O`	Michaelis constant for oxygenation (T_leaf)	\(\mu\)mol / mol	calculated
\(O\)	`O`	atmospheric O2 concentration	kPa	21.27565
\(\phi_J\)	`phi_J`	initial slope of the response of J to PPFD	none	0.331
PPFD	`PPFD`	photosynthetic photon flux density	umol quanta / (m^2 s)	1500
\(R_\mathrm{d}\)	`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
\(V_\mathrm{c,max}\)	`V_cmax`	maximum rate of carboxylation (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(V_\mathrm{tpu}\)	`V_tpu`	rate of triose phosphate utilization (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated

FvCB: Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model

Description

Usage

Value

Arguments

Details

References

Examples