PhotoGEA                The PhotoGEA R package
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
                        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_temperature_param_bernacchi
                        C3 temperature response parameters from
                        Bernacchi et al.
c3_temperature_param_flat
                        C3 temperature response parameters for a flat
                        response
c3_temperature_param_sharkey
                        C3 temperature response parameters from Sharkey
                        et al.
c4_temperature_param_flat
                        C4 temperature response parameters for a flat
                        response
c4_temperature_param_vc
                        C4 temperature response parameters from von
                        Caemmerer
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_jmax          Calculate maximum electron transport rate
calculate_leakiness_ubierna
                        Calculate leakiness
calculate_temperature_response
                        Calculate temperature-dependent parameter
                        values
calculate_temperature_response_arrhenius
                        Calculate temperature-dependent values using
                        Arrhenius equations
calculate_temperature_response_gaussian
                        Calculate temperature-dependent values using
                        Gaussian equations
calculate_temperature_response_johnson
                        Calculate temperature-dependent values using
                        Johnson-Eyring-Williams equations
calculate_temperature_response_polynomial
                        Calculate temperature-dependent values using
                        polynomial 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              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      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
csv.exdf                Read and write CSV files representing an exdf
                        object
deprecated              Deprecated functions
dim.exdf                Retrieve the dimension of an exdf object
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      Example data files
exclude_outliers        Exclude outliers from a data set
exdf                    Extended data frame
extract.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 A-Ci curve
fit_c3_variable_j       Fits a C3 assimilation model to an A-Ci + CF
                        curve
fit_c4_aci              Fits a C4 assimilation model to an A-Ci curve
fit_c4_aci_hyperbola    Fits a hyperbolic C4 assimilation model to an
                        experimental curve
fit_laisk               Calculate RL and Ci_star using the Laisk method
fit_medlyn              Fits the Medlyn 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_c3_limiting_processes
                        Identify C3 Limiting Processes
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?
jmax_temperature_param_bernacchi
                        Jmax-related temperature response parameters
                        from Bernacchi et al.
jmax_temperature_param_flat
                        Jmax-related temperature response parameters
                        from Bernacchi et al.
length.exdf             Length of an exdf object
multi_curve_colors      Set of colors for plotting multiple curves
optimizers              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_ball_berry_fit     Plot the results of a C3 CO2 response curve fit
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
plot_laisk_fit          Plot the results of a C3 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            Set values, units, and categories for a column
                        in a table
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
