Tools for Plant Ecophysiology & Modeling

Contains modeling and analytical tools for plant ecophysiology. MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer, Berry (1980) model as described in Buckley and Diaz-Espejo (2015) . 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) . 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) ) and AQ curves (Marshall & Biscoe (1980) ), temperature responses (Heskel et al. (2016) ; Kruse et al. (2008) , Medlyn et al. (2002) , Hobbs et al. (2013) ), respiration in the light (Kok (1956) , Walker & Ort (2015) , Yin et al. (2009) , Yin et al. (2011) ), mesophyll conductance (Harley et al. (1992) ), pressure-volume curves (Koide et al. (2000) , Sack et al. (2003) , Tyree et al. (1972) ), hydraulic vulnerability curves (Ogle et al. (2009) , Pammenter et al. (1998) ), and tools for running sensitivity analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(), R_d()).

photosynthesis

Model C3 Photosynthesis

Description

photosynthesis is an R package with modeling tools for C3 photosynthesis, as well as analytical tools for curve-fitting plant ecophysiology responses. It uses the R package units to ensure that parameters are properly specified and transformed before calculations.

Get photosynthesis

From CRAN

install.packages("photosynthesis")

or from GitHub

install.packages("remotes")
remotes::install_github("cdmuir/photosynthesis")

And load photosynthesis

library("photosynthesis")

Vignettes

See the following vignettes for examples of what photosynthesis can do:

• Introduction to the photosynthesis package
• Modeling C3 Photosynthesis: recommendations for common scenarios
• Fitting light response curves
• Fitting CO2 response curves
• Fitting temperature response curves
• Fitting stomatal conductance models
• Fitting light respiration
• Fitting mesophyll conductance
• Fitting pressure-volume curves
• Fitting hydraulic vulnerability curves
• Sensitivity Analysis

Contributors

• Joseph Stinziano
• Chris Muir
• Cassaundra Roback
• Demi Sargent
• Bridget Murphy
• Patrick Hudson

Comments and contributions

We welcome comments, criticisms, and especially contributions! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here:

https://github.com/cdmuir/photosynthesis/issues

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for photosynthesis in R doing citation(package = 'photosynthesis')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.