A_supply

A_demand

This function is not intended to be called by users directly.

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

A_supply 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>
<dt>use_legacy_version</dt>
<dd>Logical. Should legacy model (&lt;2.1.0) be used? See <a href="https://github.com/cdmuir/photosynthesis/blob/master/NEWS.md">NEWS</a> for further information. Default is FALSE.</dd></dl>

Arguments

CO2 supply and demand function (mol / m^2 s) — A_supply

<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>


<dt>use_legacy_version</dt>
<dd>Logical. Should legacy model (&lt;2.1.0) be used? See <a href='https://github.com/cdmuir/photosynthesis/blob/master/NEWS.md'>NEWS</a> for further information. Default is FALSE.</dd>

</dl>

Symbol	R	Description	Units	Default
\(A\)	`A`	photosynthetic rate	\(\mu\)mol CO2 / (m^2 s)	calculated
\(g_\mathrm{tc}\)	`g_tc`	total conductance to CO2	\(\mu\)mol CO2 / (m\(^2\) s Pa)	calculated
\(C_\mathrm{air}\)	`C_air`	atmospheric CO2 concentration	Pa	41
\(C_\mathrm{chl}\)	`C_chl`	chloroplastic CO2 concentration	Pa	calculated
\(R_\mathrm{d}\)	`R_d`	nonphotorespiratory CO2 release	\(\mu\)mol CO2 / (m\(^2\) s)	2
\(\Gamma*\)	`gamma_star`	chloroplastic CO2 compensation point	Pa	3.743

A_supply: CO2 supply and demand function (mol / m^2 s)

Description

Usage

Value

Arguments

Details

Examples