Plot the results of a C3 CO2 response curve fit
plot_ball_berry_fit.Rd
Plots the output from fit_c3_aci
or
fit_c3_variable_j
.
Usage
plot_ball_berry_fit(
fit_results,
identifier_column_name,
bb_index_column_name = 'bb_index',
gsw_column_name = 'gsw',
...
)
Arguments
- fit_results
A list of three
exdf
objects namesfits
,parameters
, andfits_interpolated
, as calculated byfit_c3_aci
.- 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'
.- bb_index_column_name
The name of the column in
fit_results$fits
that contains the Ball-Berry index inmol m^(-2) s^(-1)
; should be the same value that was passed tofit_ball_berry
.- gsw_column_name
The name of the column in
fit_results$fits
that contains the stomatal conductance to water vapor inmol m^(-2) s^(-1)
; should be the same value that was passed tofit_ball_berry
.- ...
Additional arguments to be passed to
xyplot
.
Details
This is a convenience function for plotting the results of a Ball-Berry 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_ball_berry
.
The resulting plot will show curves for the fitted gsw
, along with
points for the measured values of gsw
.
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_ball_berry
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, calculate
# additional gas properties, calculate the Ball-Berry index, define a new column
# that uniquely identifies each curve, and then perform a fit to extract the
# Ball-Berry parameters from each curve.
licor_file <- read_gasex_file(
PhotoGEA_example_file_path('ball_berry_1.xlsx')
)
licor_file <- calculate_total_pressure(licor_file)
licor_file <- calculate_gas_properties(licor_file)
licor_file[,'species_plot'] <-
paste(licor_file[,'species'], '-', licor_file[,'plot'])
licor_file <- calculate_ball_berry_index(licor_file)
# Fit all curves in the data set
bb_results <- consolidate(by(
licor_file,
licor_file[, 'species_plot'],
fit_ball_berry
))
# View the fits for each species / plot
plot_ball_berry_fit(bb_results, 'species_plot')