Function reference • PhotoGEA

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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_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_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_rd_laisk(): Calculate Rd using the Laisk method

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

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

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

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

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

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