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All functions

PhotoGEA_example_file_path()
Locate a PhotoGEA example file on your computer
apply_gm()
Calculate CO2 concentration in the chloroplast or mesophyll
as.data.frame(<exdf>)
Convert an exdf object to a data frame
barchart_with_errorbars() bwplot_wrapper()
Barcharts with error bars
basic_stats()
Calculate basic stats (mean and standard error)
by(<exdf>)
Apply a function to an exdf object split by one or more factors
c3_arrhenius_bernacchi
C3 Arrhenius parameters from Bernacchi et al.
c3_arrhenius_no_temp
C3 Arrhenius parameters with no temperature dependence
c3_arrhenius_sharkey
C3 Arrhenius parameters from Sharkey et al.
c4_arrhenius_no_temp
C4 Arrhenius parameters with no temperature dependence
c4_arrhenius_von_caemmerer
C4 Arrhenius parameters from von Caemmerer
c4_peaked_gaussian_no_temp
C4 peaked Gaussian parameters with no temperature response
c4_peaked_gaussian_von_caemmerer
C4 Arrhenius parameters from von Caemmerer
calculate_RL_laisk()
Calculate RL using the Laisk method
calculate_arrhenius()
Calculate temperature-dependent values using Arrhenius equations
calculate_ball_berry_index()
Calculate the Ball-Berry index
calculate_c3_assimilation()
Calculate C3 assimilation rates
calculate_c3_limitations_grassi()
Estimate the relative limiting factors to C3 photosynthesis
calculate_c3_limitations_warren()
Estimate the relative limiting factors to C3 photosynthesis
calculate_c3_variable_j()
Calculate C3 variable J
calculate_c4_assimilation()
Calculate C4 assimilation rates
calculate_c4_assimilation_hyperbola()
Calculate C4 assimilation rates using a hyperbola
calculate_gamma_star()
Calculate Gamma_star from Rubisco specificity
calculate_gas_properties()
Calculate gas properties that are typically not included in Licor files
calculate_gm_busch()
Calculate mesophyll conductance to CO2 diffusion
calculate_gm_ubierna()
Calculate mesophyll conductance to CO2 diffusion
calculate_isotope_discrimination()
Calculate photosynthetic isotope discrimination
calculate_leakiness_ubierna()
Calculate leakiness
calculate_peaked_gaussian()
Calculate temperature-dependent values using Gaussian equations
calculate_ternary_correction()
Calculate ternary correction factor
calculate_total_pressure()
Calculate the total pressure in bar
calculate_wue()
Calculate intrinsic water use efficiency
cbind(<exdf>) rbind(<exdf>)
Combine exdf objects by columns or rows
check_required_variables()
Make sure required variables exist
check_response_curve_data()
Check response curve data for common issues
choose_input_files() choose_input_licor_files() choose_input_tdl_files()
Choosing input files
confidence_intervals_c3_aci()
Calculate confidence intervals for C3 A-Ci fitting parameters
confidence_intervals_c3_variable_j()
Calculate confidence intervals for C3 Variable J fitting parameters
confidence_intervals_c4_aci()
Calculate confidence intervals for C4 A-Ci fitting parameters
confidence_intervals_c4_aci_hyperbola()
Calculate confidence intervals for C4 A-Ci hyperbola fitting parameters
consolidate()
Consolidate a list of lists
read.csv.exdf() write.csv.exdf()
Read and write CSV files representing an exdf object
read_tdl_file() read_licor_file() check_licor_data()
Deprecated functions
dim(<exdf>)
Retrieve the dimension of an exdf object
dimnames(<exdf>) `dimnames<-`(<exdf>)
Retrieve or set the dimension names of an exdf object
document_variables()
Document exdf columns by specifying units and categories
error_function_c3_aci()
Generate an error function for C3 A-Ci curve fitting
error_function_c3_variable_j()
Generate an error function for C3 Variable J curve fitting
error_function_c4_aci()
Generate an error function for C4 A-Ci curve fitting
error_function_c4_aci_hyperbola()
Generate an error function for C4 A-Ci curve fitting with a hyperbola
estimate_licor_variance()
Estimate variance of measured Licor values
estimate_operating_point()
Estimate the operating point from an A-Ci curve
example_data_files ball_berry_1 ball_berry_2 c3_aci_1 c3_aci_2 c4_aci_1 c4_aci_2 licor_for_gm_site11 licor_for_gm_site13 tdl_for_gm tdl_sampling_1 tdl_sampling_2 plaintext_licor_file plaintext_licor_file_v2 ball_berry_1.csv ball_berry_1.xlsx ball_berry_2.xlsx c3_aci_1.xlsx c3_aci_2.xlsx c4_aci_1.xlsx c4_aci_2.xlsx licor_for_gm_site11.xlsx licor_for_gm_site13.xlsx tdl_for_gm.dat tdl_sampling_1.dat tdl_sampling_2.dat
Example data files
exclude_outliers()
Exclude outliers from a data set
exdf()
Extended data frame
`[`(<exdf>) `[<-`(<exdf>)
Access or modify exdf elements
factorize_id_column()
Convert ID column to a factor with a suitable ordering
fit_ball_berry()
Fits the Ball-Berry model to an experimental curve
fit_c3_aci()
Fits a C3 assimilation model to an experimental curve
fit_c3_variable_j()
Fits a C3 assimilation model to an experimental curve
fit_c4_aci()
Fits a C4 assimilation model to an experimental curve
fit_c4_aci_hyperbola()
Fits a hyperbolic C4 assimilation model to an experimental curve
get_oxygen_from_preamble()
Extract oxygen information from a Licor file
get_sample_valve_from_filename()
Extract TDL valve information from file name
identifier_columns()
Find columns that have a single value across all rows
identify_common_columns()
Identify columns that are common to multiple objects
identify_tdl_cycles()
Identifying cycles in TDL data
initial_guess_c3_aci()
Make an initial guess of FvCB model parameter values for one curve
initial_guess_c3_variable_j()
Make an initial guess of "variable J" model parameter values for one curve
initial_guess_c4_aci()
Make an initial guess of C4 photosynthesis parameter values for one curve
initial_guess_c4_aci_hyperbola()
Make an initial guess of C4 hyperbola parameter values for one curve
is.exdf()
Is an object an exdf?
length(<exdf>)
Length of an exdf object
multi_curve_colors() multi_curve_line_colors() multi_curve_point_colors()
Set of colors for plotting multiple curves
optimizer_nmkb() optimizer_hjkb() optimizer_deoptim()
Optimizers
organize_response_curve_data()
Reorganize response curve data for analysis and plotting
pair_gasex_and_tdl()
Pair gas exchange and TDL data
pdf_print()
Print a plot object or save it to a PDF
plot_c3_aci_fit()
Plot the results of a C3 CO2 response curve fit
plot_c4_aci_fit()
Plot the results of a C4 CO2 response curve fit
plot_c4_aci_hyperbola_fit()
Plot the results of a hyperbolic C4 CO2 response curve fit
print(<exdf>)
Print the contents of an exdf object
process_tdl_cycle_erml()
Process cycles from the ERML TDL
process_tdl_cycle_polynomial()
Process TDL cycles using a polynomial correction method
read_cr3000()
Reading a CR3000 data file
read_gasex_file()
Reading a gas exchange log file
read_licor_6800_Excel()
Reading a Licor LI-6800 Excel log file
read_licor_6800_plaintext()
Reading a Licor LI-6800 plaintext log file
remove_points()
Remove specific points from an exdf object
residual_stats()
Calculate statistics that describe the residuals of a fit
set_variable()
Document exdf columns by specifying units and categories
smooth_tdl_data()
Smoothing data from one TDL valve
split(<exdf>)
Divide an exdf object into groups
str(<exdf>)
Display the structure of an exdf object
xyplot_avg_rc()
Plot average response curves with error bars