get_default_model

get_all_models

marshall_biscoe_1980

<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=photosynthesis&version=2.1.1" alt="[Experimental]"></a>
Get the name of the default model used for different plant ecophysiological data analysis methods implemented in photosynthesis. Currently only used for <code>fit_aq_response2</code> and <code>fit_r_light2</code>.
Light response models:<ul>
<li><code>marshall_biscoe_1980()</code>: Non-rectangular hyperbolic model of light responses</li>
</ul>

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

get_default_model function

<dl><dt>.photo_fun</dt>
<dd>A character string of photosynthesis function to call. One of: <code>aq_response, r_light</code>.</dd>
<dt>method</dt>
<dd>A character string of the statistical method to use: 'ls' for least-squares and 'brms' for Bayesian model using <code>brm</code>. Default is 'ls'.</dd>
<dt>Q_abs</dt>
<dd>Absorbed light intensity (\(\mu\)mol m\(^{-2}\) s\(^{-1}\))</dd>
<dt>k_sat</dt>
<dd>Light saturated rate of process k</dd>
<dt>phi_J</dt>
<dd>Quantum efficiency of process k</dd>
<dt>theta_J</dt>
<dd>Curvature of the light response</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a>
Get the name of the default model used for different plant ecophysiological data analysis methods implemented in photosynthesis. Currently only used for <code>fit_aq_response2</code> and <code>fit_r_light2</code>.
Light response models:<ul>
<li><code>marshall_biscoe_1980()</code>: Non-rectangular hyperbolic model of light responses</li>
</ul>

Get default model — get_default_model

<dl>

<dt>.photo_fun</dt>
<dd>A character string of photosynthesis function to call. One of: <code>aq_response, r_light</code>.</dd>


<dt>method</dt>
<dd>A character string of the statistical method to use: 'ls' for least-squares and 'brms' for Bayesian model using <code>brm</code>. Default is 'ls'.</dd>


<dt>Q_abs</dt>
<dd>Absorbed light intensity (\(\mu\)mol m\(^{-2}\) s\(^{-1}\))</dd>


<dt>k_sat</dt>
<dd>Light saturated rate of process k</dd>


<dt>phi_J</dt>
<dd>Quantum efficiency of process k</dd>


<dt>theta_J</dt>
<dd>Curvature of the light response</dd>

</dl>

get_default_model: Get default model

Description

Usage

Value

Arguments

Examples