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).

Tools for Plant Ecophysiology & Modeling

package-ubuntu-20.04-r-4.0.5#cran#photosynthesis-2.0.0

package-ubuntu-20.04-r-4.0.5#cran#photosynthesis-2.0.0#docs#baked-class

baked-class

Description

photosynthesis

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