Man pages for PhotoGEA
Photosynthetic Gas Exchange Analysis
| 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... |
| 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... |
| 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... |
| calculate_temperature_response_gaussian | Calculate temperature-dependent values using Gaussian... |
| calculate_temperature_response_johnson | Calculate temperature-dependent values using... |
| calculate_temperature_response_polynomial | Calculate temperature-dependent values using polynomial... |
| 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... |
| 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... |
| 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... |
| 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... |
| 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... |
| initial_guess_c3_variable_j | Make an initial guess of "Variable J" model parameter values... |
| initial_guess_c4_aci | Make an initial guess of C4 photosynthesis parameter values... |
| initial_guess_c4_aci_hyperbola | Make an initial guess of C4 hyperbola parameter values for... |
| is.exdf | Is an object an exdf? |
| jmax_temperature_param_bernacchi | Jmax-related temperature response parameters from Bernacchi... |
| jmax_temperature_param_flat | Jmax-related temperature response parameters from Bernacchi... |
| 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 |
| PhotoGEA | The PhotoGEA R package |
| PhotoGEA_example_file_path | Locate a PhotoGEA example file on your computer |
| 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 |
