Calculate the rate of electron transport as a function of photosynthetic photon flux density (PPFD).

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

J function

<dl><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

J: Rate of electron transport (umol/m^2/s) — J

<dl>

<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>

Symbol	R	Description	Units	Default
\(J_\mathrm{max}\)	`J_max`	potential electron transport (T_leaf)	\(\mu\)mol CO2 / (m\(^2\) s)	calculated
\(\phi_J\)	`phi_J`	initial slope of the response of J to PPFD	none	0.331
PPFD	`PPFD`	photosynthetic photon flux density	\(\mu\)mol quanta / (m^2 s)	1500
\(\theta_J\)	`theta_J`	curvature factor for light-response curve	none	0.825

J: J: Rate of electron transport (umol/m^2/s)

Description

Usage

Value

Arguments

Details

Examples