Photosynthetic Gas Exchange Analysis

Documentation for package ‘PhotoGEA’ version 1.3.3

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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