plantecophys (version 0.6-3)

fitBBOpti: Fit the BBOpti stomatal conductance model.

Description

This function fits the stomatal conductance model of Medlyn et al. (2011) to leaf gas exchange data using non-linear regression. See Details (below) for instructions on how to organize your data, and how to interpret the output. This is a very user-friendly interface to fitting the model, useful for novice R users. For more advanced users, it is probably best to fit the model with nls yourself (see Details).

Usage

fitBBOpti(filename = NULL)

Arguments

filename

Name of the CSV file (optional).

Details

The following function is fit, using non-linear regression: gs = g0 + 1.6*(1 + g1/sqrt(D)) * (A/Ca) Where :

• gs- Stomatal conductance to H2O (mol m-2 s-1)
• D- Vapor pressure deficit (kPa)
• A- Leaf net photosynthesis (mu mol m-2 s-1)
• Ca- Ambient CO2 concentration (ppm)
• g0,g1- The fitted parameters

The data needs to be saved in a CSV (comma-separated values) file, with the following four columns (these are the header names that the program uses to find the variables): A, gs, Ca and D (or VPD) in *exactly* the same units as in the table above. If #' you are unsure on how to organize your data, just send an email to the package maintainer to receive an example CSV file. Once you have the data organized properly, simply type the following command: fitBBOpti() Menus and messages guide you through the process of fitting the model to your data. Optionally, the fitted stomatal conductance values of the model are saved in the #'same CSV file, and saved in the same folder as the original CSV file. The new CSV file has the suffix _R. The fitBBOpti function is a very user-friendly interface without any options. If you want more control, run the non-linear regression yourself, with this command: nlsfit <- nls(g ~ g0 + 1.6*(1+g1/sqrt(D))*(A/Ca),start=list(g0=0.02, g1=8), data=mydataframe) where mydataframe is a dataframe that contains the variables A,Ca and D.

Examples

fitBBOpti("myfile.csv")