plot_c4_aci_hyperbola_fit: Plot the results of a hyperbolic C4 CO2 response curve fit

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Plot the results of a hyperbolic C4 CO2 response curve fit

Description

Plots the output from fit_c4_aci_hyperbola.

Usage

  plot_c4_aci_hyperbola_fit(
    fit_results,
    identifier_column_name,
    a_column_name = 'A',
    ci_column_name = 'Ci',
    ...
  )

Arguments

fit_results	A list of three exdf objects named fits, parameters, and fits_interpolated, as calculated by fit_c4_aci_hyperbola.
identifier_column_name	The name of a column in each element of fit_results whose value can be used to identify each response curve within the data set; often, this is 'curve_identifier'.
a_column_name	The name of the columns in the elements of fit_results that contain the net assimilation in micromol m^(-2) s^(-1); should be the same value that was passed to fit_c4_aci_hyperbola.
ci_column_name	The name of the columns in the elements of fit_results that contain the intercellular CO2 concentration in micromol mol^(-1); should be the same value that was passed to fit_c4_aci_hyperbola.
...	Additional arguments to be passed to xyplot.

Details

This is a convenience function for plotting the results of a C4 A-Ci curve fit. It is typically used for displaying several fits at once, in which case fit_results is actually the output from calling consolidate on a list created by calling by.exdf with FUN = fit_c4_aci_hyperbola.

The resulting plot will show curves for the fitted rates An, Ainitial, and Amax, along with points for the measured values of A.

Internally, this function uses xyplot to perform the plotting. Optionally, additional arguments can be passed to xyplot. These should typically be limited to things like xlim, ylim, main, and grid, since many other xyplot arguments will be set internally (such as xlab, ylab, auto, and others).

See the help file for fit_c4_aci_hyperbola for an example using this function.

Value

A trellis object created by lattice::xyplot.

Examples

# Read an example Licor file included in the PhotoGEA package
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('c4_aci_1.xlsx')
)

# Define a new column that uniquely identifies each curve
licor_file[, 'species_plot'] <-
  paste(licor_file[, 'species'], '-', licor_file[, 'plot'] )

# Organize the data
licor_file <- organize_response_curve_data(
    licor_file,
    'species_plot',
    c(9, 10, 16),
    'CO2_r_sp'
)

# Fit all curves in the data set
aci_results <- consolidate(by(
  licor_file,
  licor_file[, 'species_plot'],
  fit_c4_aci_hyperbola
))

# View the fits for each species / plot
plot_c4_aci_hyperbola_fit(aci_results, 'species_plot', ylim = c(0, 100))

PhotoGEA documentation built on Aug. 25, 2025, 5:13 p.m.