# Photosynthetic Gas Exchange Analysis

## Documentation for package ‘PhotoGEA’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I J L M O P R S T W X misc

## -- A --

apply_gm | Calculate CO2 concentration in the chloroplast or mesophyll
as.data.frame.exdf | Convert an exdf object to a data frame

## -- B --

ball_berry_1 | Example data files
ball_berry_1.csv | Example data files
ball_berry_1.xlsx | Example data files
ball_berry_2 | Example data files
ball_berry_2.xlsx | Example data files
barchart_with_errorbars | Barcharts with error bars
basic_stats | Calculate basic stats (mean and standard error)
bwplot_wrapper | Barcharts with error bars
by.exdf | Apply a function to an exdf object split by one or more factors

## -- C --

c3_aci_1 | Example data files
c3_aci_1.xlsx | Example data files
c3_aci_2 | Example data files
c3_aci_2.xlsx | Example data files
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_aci_1 | Example data files
c4_aci_1.xlsx | Example data files
c4_aci_2 | Example data files
c4_aci_2.xlsx | Example data files
c4_temperature_param_flat | C4 temperature response parameters for a flat response
c4_temperature_param_vc | C4 temperature response parameters from von Caemmerer
calculate_arrhenius | Deprecated functions
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_peaked_gaussian | Deprecated functions
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_licor_data | Deprecated functions
check_required_variables | Make sure required variables exist
check_required_variables.data.frame | Make sure required variables exist
check_required_variables.exdf | Make sure required variables exist
check_response_curve_data | Check response curve data for common issues
choose_input_files | Choosing input files
choose_input_licor_files | Choosing input 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
consolidate.data.frame | Consolidate a list of lists
consolidate.exdf | Consolidate a list of lists
csv.exdf | Read and write CSV files representing an exdf object

## -- D --

deprecated | Deprecated functions
dim.exdf | Retrieve the dimension of an exdf object
dimnames.exdf | Retrieve or set the dimension names 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
document_variables.data.frame | Document exdf columns by specifying units and categories
document_variables.exdf | Document exdf columns by specifying units and categories

## -- E --

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
exclude_outliers.data.frame | Exclude outliers from a data set
exclude_outliers.exdf | Exclude outliers from a data set
exdf | Extended data frame
extract.exdf | Access or modify exdf elements

## -- F --

factorize_id_column | Convert ID column to a factor with a suitable ordering
factorize_id_column.character | Convert ID column to a factor with a suitable ordering
factorize_id_column.data.frame | Convert ID column to a factor with a suitable ordering
factorize_id_column.exdf | 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

## -- G --

get_oxygen_from_preamble | Extract oxygen information from a Licor file
get_sample_valve_from_filename | Extract TDL valve information from file name

## -- I --

identifier_columns | Find columns that have a single value across all rows
identifier_columns.data.frame | Find columns that have a single value across all rows
identifier_columns.exdf | 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_common_columns.data.frame | Identify columns that are common to multiple objects
identify_common_columns.exdf | 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?

## -- J --

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.

## -- L --

length.exdf | Length of an exdf object
licor_for_gm_site11 | Example data files
licor_for_gm_site11.xlsx | Example data files
licor_for_gm_site13 | Example data files
licor_for_gm_site13.xlsx | Example data files

## -- M --

multi_curve_colors | Set of colors for plotting multiple curves
multi_curve_line_colors | Set of colors for plotting multiple curves
multi_curve_point_colors | Set of colors for plotting multiple curves

## -- O --

optimizers | Optimizers
optimizer_deoptim | Optimizers
optimizer_hjkb | Optimizers
optimizer_nlminb | Optimizers
optimizer_nmkb | Optimizers
optimizer_null | Optimizers
organize_response_curve_data | Reorganize response curve data for analysis and plotting

## -- P --

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 | The PhotoGEA R package
PhotoGEA_example_file_path | Locate a PhotoGEA example file on your computer
plaintext_licor_file | Example data files
plaintext_licor_file_v2 | Example data files
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

## -- R --

rbind.exdf | Combine exdf objects by columns or rows
read.csv.exdf | Read and write CSV files representing an exdf object
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
read_licor_file | Deprecated functions
read_tdl_file | Deprecated functions
remove_points | Remove specific points from an exdf object
residual_stats | Calculate statistics that describe the residuals of a fit

## -- S --

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

## -- T --

tdl_for_gm | Example data files
tdl_for_gm.dat | Example data files
tdl_sampling_1 | Example data files
tdl_sampling_1.dat | Example data files
tdl_sampling_2 | Example data files
tdl_sampling_2.dat | Example data files

## -- W --

write.csv.exdf | Read and write CSV files representing an exdf object

## -- X --

xyplot_avg_rc | Plot average response curves with error bars

## -- misc --

[.exdf | Access or modify exdf elements
[<-.exdf | Access or modify exdf elements