fit_photosynthesis: Fit photosynthetic models with gas-exchange data

In cdmuir/photosynthesis: Tools for Plant Ecophysiology & Modeling

Fit photosynthetic models with gas-exchange data

Description

Fit photosynthetic models with gas-exchange data

Usage

fit_photosynthesis(
  .data,
  .photo_fun,
  .model = "default",
  .vars = NULL,
  .method = "ls",
  ...,
  quiet = FALSE,
  brm_options = NULL
)

Arguments

.data	A data frame containing plant ecophysiological data. See required_variables() for the variables required for each model.
.photo_fun	A character string of photosynthesis function to call. One of: ⁠aq_response, r_light⁠.
.model	A character string of model name to use. See get_all_models().
.vars	A list to rename variables in .data. See required_variables() for the accepted variable names.
.method	A character string of the statistical method to use: 'ls' for least-squares and 'brms' for Bayesian model using brms::brm(). Default is 'ls'.
...	Additional arguments passed to specific models. See specific help pages for each type of photosynthetic model: Light-response curves fit_aq_response2() Light respiration fit_r_light2()
quiet	Flag. Should messages be suppressed? Default is FALSE.
brm_options	A list of options passed to brms::brm() if .method = "brms". Default is NULL.

Value

A fitted model object

• class 'lm' or 'nls' if method = 'ls'

• class 'brmsfit' if method = 'brms'

Note

This function will fit models to data but several methods require post-processing to extract meaningful parameter estimates and confidence intervals. See vignettes for further explanation and examples.

• Light-response curves: vignette("light-response", package = "photosynthesis")

• Light respiration: vignette("light-respiration", package = "photosynthesis")

cdmuir/photosynthesis documentation built on April 11, 2025, 3:28 p.m.