Package: PhotoGEA 1.4.0

PhotoGEA: Photosynthetic Gas Exchange Analysis

Read, process, fit, and analyze photosynthetic gas exchange measurements. Documentation is provided by several vignettes; also see Lochocki, Salesse-Smith, & McGrath (2025) <doi:10.1111/pce.15501>.

Authors:Edward B. Lochocki [cre, aut], Coralie E. Salesse-Smith [aut], Justin M. McGrath [aut], PhotoGEA authors [cph]

PhotoGEA_1.4.0.tar.gz
PhotoGEA_1.4.0.zip(r-4.7-any)PhotoGEA_1.4.0.zip(r-4.6-any)PhotoGEA_1.4.0.zip(r-4.5-any)
PhotoGEA_1.4.0.tgz(r-4.6-any)PhotoGEA_1.4.0.tgz(r-4.5-any)
PhotoGEA_1.4.0.tar.gz(r-4.7-any)PhotoGEA_1.4.0.tar.gz(r-4.6-any)
PhotoGEA_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhotoGEA/json (API)

# Install 'PhotoGEA' in R:

install.packages('PhotoGEA', repos = c('https://eloch216.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eloch216/photogea/issues

Pkgdown/docs site:https://eloch216.github.io

Datasets:

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
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.

On CRAN:

5.29 score 8 stars 49 scripts 289 downloads 127 exports 8 dependencies

Last updated from:947709bed9. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	270
source / vignettes	OK	207
linux-release	OK	278
macos-release	OK	220
macos-oldrel	OK	267
windows-devel	OK	257
windows-release	OK	264
windows-oldrel	OK	270
wasm-release	OK	123

Exports:[.exdf [<-.exdf apply_gm as.data.frame.exdf barchart_with_errorbars basic_stats bwplot_wrapper by.exdf calculate_arrhenius calculate_ball_berry_index calculate_c3_assimilation calculate_c3_limitations_grassi calculate_c3_limitations_warren calculate_c3_variable_j calculate_c4_assimilation calculate_c4_assimilation_hyperbola calculate_gamma_star calculate_gas_properties calculate_gm_busch calculate_gm_ubierna calculate_isotope_discrimination calculate_jmax calculate_leakiness_ubierna calculate_peaked_gaussian calculate_temperature_response calculate_temperature_response_arrhenius calculate_temperature_response_gaussian calculate_temperature_response_johnson calculate_temperature_response_polynomial calculate_ternary_correction calculate_total_pressure calculate_wue cbind.exdf check_licor_data check_required_variables check_required_variables.data.frame check_required_variables.exdf check_response_curve_data choose_input_files choose_input_licor_files choose_input_tdl_files confidence_intervals_c3_aci confidence_intervals_c3_variable_j confidence_intervals_c4_aci confidence_intervals_c4_aci_hyperbola consolidate consolidate.data.frame consolidate.exdf dim.exdf dimnames.exdf dimnames<-.exdf document_variables document_variables.data.frame document_variables.exdf error_function_c3_aci error_function_c3_variable_j error_function_c4_aci error_function_c4_aci_hyperbola estimate_licor_variance estimate_operating_point exclude_outliers exclude_outliers.data.frame exclude_outliers.exdf exdf factorize_id_column factorize_id_column.character factorize_id_column.data.frame factorize_id_column.exdf fit_ball_berry fit_c3_aci fit_c3_variable_j fit_c4_aci fit_c4_aci_hyperbola fit_laisk fit_medlyn get_oxygen_from_preamble get_sample_valve_from_filename identifier_columns identifier_columns.data.frame identifier_columns.exdf identify_c3_limiting_processes identify_common_columns identify_common_columns.data.frame identify_common_columns.exdf identify_tdl_cycles initial_guess_c3_aci initial_guess_c3_variable_j initial_guess_c4_aci initial_guess_c4_aci_hyperbola is.exdf length.exdf multi_curve_colors multi_curve_line_colors multi_curve_point_colors optimizer_deoptim optimizer_hjkb optimizer_nlminb optimizer_nmkb optimizer_null organize_response_curve_data pair_gasex_and_tdl pdf_print PhotoGEA_example_file_path plot_ball_berry_fit plot_c3_aci_fit plot_c4_aci_fit plot_c4_aci_hyperbola_fit plot_laisk_fit print.exdf process_tdl_cycle_erml process_tdl_cycle_polynomial rbind.exdf read_cr3000 read_gasex_file read_licor_6800_Excel read_licor_6800_plaintext read_licor_file read_tdl_file read.csv.exdf remove_points residual_stats set_variable smooth_tdl_data split.exdf str.exdf write.csv.exdf xyplot_avg_rc

Dependencies:cli DEoptim dfoptim lattice openxlsx Rcpp stringi zip

Getting Started With PhotoGEA

Overview | Installing PhotoGEA | Using PhotoGEA

Rendered fromPhotoGEA.Rmdusingknitr::rmarkdown

Last update: 2025-08-04
Started: 2022-09-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate CO2 concentration in the chloroplast or mesophyll	apply_gm
Convert an exdf object to a data frame	as.data.frame.exdf
Barcharts with error bars	barchart_with_errorbars bwplot_wrapper
Calculate basic stats (mean and standard error)	basic_stats
Apply a function to an exdf object split by one or more factors	by.exdf
C3 temperature response parameters from Bernacchi et al.	c3_temperature_param_bernacchi
C3 temperature response parameters for a flat response	c3_temperature_param_flat
C3 temperature response parameters from Sharkey et al.	c3_temperature_param_sharkey
C4 temperature response parameters for a flat response	c4_temperature_param_flat
C4 temperature response parameters from von Caemmerer	c4_temperature_param_vc
Calculate the Ball-Berry index	calculate_ball_berry_index
Calculate C3 assimilation rates	calculate_c3_assimilation
Estimate the relative limiting factors to C3 photosynthesis	calculate_c3_limitations_grassi
Estimate the relative limiting factors to C3 photosynthesis	calculate_c3_limitations_warren
Calculate C3 variable J	calculate_c3_variable_j
Calculate C4 assimilation rates	calculate_c4_assimilation
Calculate C4 assimilation rates using a hyperbola	calculate_c4_assimilation_hyperbola
Calculate Gamma_star from Rubisco specificity	calculate_gamma_star
Calculate gas properties that are typically not included in Licor files	calculate_gas_properties
Calculate mesophyll conductance to CO2 diffusion	calculate_gm_busch
Calculate mesophyll conductance to CO2 diffusion	calculate_gm_ubierna
Calculate photosynthetic isotope discrimination	calculate_isotope_discrimination
Calculate maximum electron transport rate	calculate_jmax
Calculate leakiness	calculate_leakiness_ubierna
Calculate temperature-dependent parameter values	calculate_temperature_response
Calculate temperature-dependent values using Arrhenius equations	calculate_temperature_response_arrhenius
Calculate temperature-dependent values using Gaussian equations	calculate_temperature_response_gaussian
Calculate temperature-dependent values using Johnson-Eyring-Williams equations	calculate_temperature_response_johnson
Calculate temperature-dependent values using polynomial equations	calculate_temperature_response_polynomial
Calculate ternary correction factor	calculate_ternary_correction
Calculate the total pressure in bar	calculate_total_pressure
Calculate intrinsic water use efficiency	calculate_wue
Combine exdf objects by columns or rows	cbind.exdf rbind.exdf
Make sure required variables exist	check_required_variables check_required_variables.data.frame check_required_variables.exdf
Check response curve data for common issues	check_response_curve_data
Choosing input files	choose_input_files choose_input_licor_files choose_input_tdl_files
Calculate confidence intervals for C3 A-Ci fitting parameters	confidence_intervals_c3_aci
Calculate confidence intervals for C3 Variable J fitting parameters	confidence_intervals_c3_variable_j
Calculate confidence intervals for C4 A-Ci fitting parameters	confidence_intervals_c4_aci
Calculate confidence intervals for C4 A-Ci hyperbola fitting parameters	confidence_intervals_c4_aci_hyperbola
Consolidate a list of lists	consolidate consolidate.data.frame consolidate.exdf
Read and write CSV files representing an exdf object	csv.exdf read.csv.exdf write.csv.exdf
Deprecated functions	calculate_arrhenius calculate_peaked_gaussian check_licor_data deprecated read_licor_file read_tdl_file
Retrieve the dimension of an exdf object	dim.exdf
Retrieve or set the dimension names of an exdf object	dimnames.exdf dimnames<-.exdf
Document exdf columns by specifying units and categories	document_variables document_variables.data.frame document_variables.exdf
Generate an error function for C3 A-Ci curve fitting	error_function_c3_aci
Generate an error function for C3 Variable J curve fitting	error_function_c3_variable_j
Generate an error function for C4 A-Ci curve fitting	error_function_c4_aci
Generate an error function for C4 A-Ci curve fitting with a hyperbola	error_function_c4_aci_hyperbola
Estimate variance of measured Licor values	estimate_licor_variance
Estimate the operating point from an A-Ci curve	estimate_operating_point
Example data files	ball_berry_1 ball_berry_1.csv ball_berry_1.xlsx ball_berry_2 ball_berry_2.xlsx c3_aci_1 c3_aci_1.xlsx c3_aci_2 c3_aci_2.xlsx c4_aci_1 c4_aci_1.xlsx c4_aci_2 c4_aci_2.xlsx example_data_files licor_for_gm_site11 licor_for_gm_site11.xlsx licor_for_gm_site13 licor_for_gm_site13.xlsx plaintext_licor_file plaintext_licor_file_v2 tdl_for_gm tdl_for_gm.dat tdl_sampling_1 tdl_sampling_1.dat tdl_sampling_2 tdl_sampling_2.dat
Exclude outliers from a data set	exclude_outliers exclude_outliers.data.frame exclude_outliers.exdf
Extended data frame	exdf
Access or modify exdf elements	extract.exdf [.exdf [<-.exdf
Convert ID column to a factor with a suitable ordering	factorize_id_column factorize_id_column.character factorize_id_column.data.frame factorize_id_column.exdf
Fits the Ball-Berry model to an experimental curve	fit_ball_berry
Fits a C3 assimilation model to an A-Ci curve	fit_c3_aci
Fits a C3 assimilation model to an A-Ci + CF curve	fit_c3_variable_j
Fits a C4 assimilation model to an A-Ci curve	fit_c4_aci
Fits a hyperbolic C4 assimilation model to an experimental curve	fit_c4_aci_hyperbola
Calculate RL and Ci_star using the Laisk method	fit_laisk
Fits the Medlyn model to an experimental curve	fit_medlyn
Extract oxygen information from a Licor file	get_oxygen_from_preamble
Extract TDL valve information from file name	get_sample_valve_from_filename
Find columns that have a single value across all rows	identifier_columns identifier_columns.data.frame identifier_columns.exdf
Identify C3 Limiting Processes	identify_c3_limiting_processes
Identify columns that are common to multiple objects	identify_common_columns identify_common_columns.data.frame identify_common_columns.exdf
Identifying cycles in TDL data	identify_tdl_cycles
Make an initial guess of FvCB model parameter values for one curve	initial_guess_c3_aci
Make an initial guess of "Variable J" model parameter values for one curve	initial_guess_c3_variable_j
Make an initial guess of C4 photosynthesis parameter values for one curve	initial_guess_c4_aci
Make an initial guess of C4 hyperbola parameter values for one curve	initial_guess_c4_aci_hyperbola
Is an object an exdf?	is.exdf
Jmax-related temperature response parameters from Bernacchi et al.	jmax_temperature_param_bernacchi
Jmax-related temperature response parameters from Bernacchi et al.	jmax_temperature_param_flat
Length of an exdf object	length.exdf
Set of colors for plotting multiple curves	multi_curve_colors multi_curve_line_colors multi_curve_point_colors
Optimizers	optimizers optimizer_deoptim optimizer_hjkb optimizer_nlminb optimizer_nmkb optimizer_null
Reorganize response curve data for analysis and plotting	organize_response_curve_data
Pair gas exchange and TDL data	pair_gasex_and_tdl
Print a plot object or save it to a PDF	pdf_print
The PhotoGEA R package	PhotoGEA photogea
Locate a PhotoGEA example file on your computer	PhotoGEA_example_file_path
Plot the results of a C3 CO2 response curve fit	plot_ball_berry_fit
Plot the results of a C3 CO2 response curve fit	plot_c3_aci_fit
Plot the results of a C4 CO2 response curve fit	plot_c4_aci_fit
Plot the results of a hyperbolic C4 CO2 response curve fit	plot_c4_aci_hyperbola_fit
Plot the results of a C3 CO2 response curve fit	plot_laisk_fit
Print the contents of an exdf object	print.exdf
Process cycles from the ERML TDL	process_tdl_cycle_erml
Process TDL cycles using a polynomial correction method	process_tdl_cycle_polynomial
Reading a CR3000 data file	read_cr3000
Reading a gas exchange log file	read_gasex_file
Reading a Licor LI-6800 Excel log file	read_licor_6800_Excel
Reading a Licor LI-6800 plaintext log file	read_licor_6800_plaintext
Remove specific points from an exdf object	remove_points
Calculate statistics that describe the residuals of a fit	residual_stats
Set values, units, and categories for a column in a table	set_variable
Smoothing data from one TDL valve	smooth_tdl_data
Divide an exdf object into groups	split.exdf
Display the structure of an exdf object	str.exdf
Plot average response curves with error bars	xyplot_avg_rc