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The plantecophys R package

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Welcome to the home of plantecophys, an R package that bundles a number of tools to analyze and model leaf gas exchange data.

Please report bugs or suggest features here.

Contents

  • fitaci and fitacis fit the Farquhar-von Caemmerer-Berry model of photosynthesis to observations of photosynthesis (A) and Ci as measured with a Licor 6400 or similar instrument.
  • fitBB fits various forms of the Ball-Berry stomatal conductance model to data.
  • Photosyn is an implementation of a coupled leaf gas exchange model, including the Farquhar-Berry-von Caemmerer model of photosynthesis, and Ball-Berry-type stomatal conductance models. Accounts for leaf temperature effects on many processes.
  • PhotosynEB is the same, but also calculates the leaf temperature (Tleaf) by solving the leaf energy balance (and takes air temperature as input). Extra inputs are wind speed, leaf width, and some others.
  • Aci calculates the dependence of photosynthesis (A) on the intercellular CO2 concentration (Ci) for C3 plants with the FvCB model (as used by fitaci)
  • FARAO is an implementation of the stomatal optimization model as suggested by Cowan and Farquhar (1977). It is a full numerical solution to the model, and uses the FARquhar model for photosynthesis.
  • The functions RHtoVPD, VPDtoRH, and DewtoVPDconvert between relative humidity, vapour pressure deficit (VPD) and the dewpoint.

Citation

Duursma, R.A., 2015. Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data. PLoS ONE 10, e0143346. doi:10.1371/journal.pone.0143346.

Help

Please read the built-in help files carefully if you have any questions. The examples are often helpful as well.

The package includes two vignettes at the moment, which can be accessed from these links:

Frequently asked questions (FAQ) on fitting A-Ci curves.

A quick introduction to fitaci.

Installation

The package is on CRAN, so just do:

install.packages("plantecophys")

To install the development version, use the following command. Windows users must have Rtools installed.

library(devtools)
install_bitbucket("remkoduursma/plantecophys")

For questions, comments, and suggestions, please email remkoduursma@gmail.com