Tools for Plant Ecophysiology & Modeling
CO2 supply and demand function (mol / m^2 s)
Running 2-parameter sensitivity analyses
Non-rectangular hyperbolic model of light responses
Leaf parameter temperature responses
S3 class bake_par
S3 class baked
Get default functions for calculated parameters in photosynthesis
Conductance to CO2 (mol / m^2 / s)
Compiling outputs from lists
Computing measures of sensitivity
S3 class constants
S3 class enviro_par
Fitting ACi curves
Fitting light responses of net CO2 assimilation
Fit photosynthetic light-response curves
Fitting mesophyll conductance with the variable J method
Fitting stomatal conductance models
Fitting hydraulic vulnerability curves
Fitting many functions across groups
Fit photosynthetic models with gas-exchange data
Fitting pressure-volume curves
Estimating light respiration
Fit models to estimate light respiration ()
Fitting temperature responses
Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
Stomatal conductance models
J: Rate of electron transport (umol/m^2/s)
Inverse non-rectangular hyperbola for J_max calculation
S3 class leaf_par
Make lists of parameters for photosynthesis
Get default model
Get vector of parameter names
photosynthesis package
Simulate C3 photosynthesis
Convert pressure from PPM to Pascals
Printing graphs to system
Read a LI-COR file
Read a LI-COR file
Variables required for photosynthesis models
Simulate gas exchange data with measurement error
Temperature response functions
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()).
Useful links