title: Plantecophys--An R Package for Analysing and Modelling Leaf Gas Exchange Data.
abstract: Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO2 in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO2 response curves ('A-Ci curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.
authors.affiliation: Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
authors.forename: Remko A
authors.initials: RA
authors.lastname: Duursma
mesh_terms: D005052:Eucalyptus / Q000502:physiology; D005740:Gases / Q000378:metabolism*; D008954:Models, Biological; D009716:Numerical Analysis, Computer-Assisted; D010788:Photosynthesis; D018515:Plant Leaves / Q000502:physiology*; D054046:Plant Stomata / Q000502:physiology; D012984:Software
chemical_list: D005740:Gases