PhotoGEA (version 1.4.0)

plot_laisk_fit: Plot the results of a C3 CO2 response curve fit

Description

Plots the output from fit_laisk.

Usage

plot_laisk_fit(
    fit_results,
    identifier_column_name,
    plot_type,
    cols = multi_curve_colors(),
    a_column_name = 'A',
    ci_column_name = 'Ci',
    ppfd_column_name = 'PPFD',
    ...
  )

Value

A trellis object created by lattice::xyplot.

Arguments

fit_results

A list of four exdf objects named first_fits, first_fit_parameters, second_fits, and second_fit_parameters, as calculated by fit_laisk.

identifier_column_name

The name of a column in each element of fit_results whose value can be used to identify each replicate within the data set; often, this is 'curve_identifier'.

plot_type

Must be either 'first' or 'second' (case-insensitive); determines which type of plot to create (see below for details).

cols

A vector of color specifications to use for each light level when plotting.

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_laisk.

ci_column_name

The name of the column 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_laisk.

ppfd_column_name

The name of the column in the elements of fit_results that can be used to split the data into individual response curves; should be the same value that was passed to fit_laisk.

...

Additional arguments to be passed to xyplot.

Details

This is a convenience function for plotting the results of a Laisk 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_laisk.

Because the Laisk fitting process involves two sets of linear fits, there are two possible graphs that can be created. When plot_type is 'first', this function will plot the individual A-Ci curves at each PPFD, along with the linear fits and the estimated intersection point. When plot_type is 'second', this function will plot the Laisk intercept vs. Laisk slope from the results of the first fits, along with a linear fit of Laisk intercept vs. Laisk slope. See fit_laisk for more details.

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_laisk for an example using this function.

Examples

# Read an example Licor file included in the PhotoGEA package
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('c3_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'
)

# Apply the Laisk method. Note: this is a bad example because these curves were
# measured at the same light intensity, but from different species. Because of
# this, the results are not meaningful.
laisk_results <- fit_laisk(
  licor_file, 20, 150,
  ppfd_column_name = 'species_plot'
)

# Plot the linear fits of A vs. Ci
plot_laisk_fit(laisk_results, 'instrument', 'first', ppfd_column_name = 'species_plot')

# Plot the linear fits of Laisk intercept vs. Laisk slope
plot_laisk_fit(laisk_results, 'instrument', 'second', ppfd_column_name = 'species_plot')