PhotoGEA
Photosynthetic Gas Exchange Analysis

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PhotoGEA: Photosynthetic Gas Exchange Analysis
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API

API for PhotoGEA
Photosynthetic Gas Exchange Analysis

Global functions
A_limiting Source code
PhotoGEA Man page
PhotoGEA_example_file_path Man page Source code
[.exdf Man page
[<-.exdf Man page
`[.exdf` Source code
`[<-.exdf` Source code
`dimnames<-.exdf` Source code
add_latest_remark Source code
apply_gm Man page Source code
arrhenius Source code
as.data.frame.exdf Man page Source code
assemble_luf Source code
ball_berry_1 Man page
ball_berry_1.csv Man page
ball_berry_1.xlsx Man page
ball_berry_2 Man page
ball_berry_2.xlsx Man page
barchart_with_errorbars Man page Source code
basic_stats Man page Source code
basic_stats_chunk Source code
bwplot_wrapper Man page Source code
by.exdf Man page Source code
c3_aci_1 Man page
c3_aci_1.xlsx Man page
c3_aci_2 Man page
c3_aci_2.xlsx Man page
c3_limitation_grassi Source code
c3_limitation_warren Source code
c3_temperature_param_bernacchi Man page
c3_temperature_param_flat Man page
c3_temperature_param_sharkey Man page
c4_aci_1 Man page
c4_aci_1.xlsx Man page
c4_aci_2 Man page
c4_aci_2.xlsx Man page
c4_temperature_param_flat Man page
c4_temperature_param_vc Man page
calculate_arrhenius Man page Source code
calculate_ball_berry_index Man page Source code
calculate_c3_assimilation Man page Source code
calculate_c3_limitations_grassi Man page Source code
calculate_c3_limitations_warren Man page Source code
calculate_c3_variable_j Man page Source code
calculate_c4_assimilation Man page Source code
calculate_c4_assimilation_hyperbola Man page Source code
calculate_gamma_star Man page Source code
calculate_gas_properties Man page Source code
calculate_gm_busch Man page Source code
calculate_gm_ubierna Man page Source code
calculate_isotope_discrimination Man page Source code
calculate_jmax Man page Source code
calculate_leakiness_ubierna Man page Source code
calculate_peaked_gaussian Man page Source code
calculate_residuals Source code
calculate_temperature_response Man page Source code
calculate_temperature_response_arrhenius Man page Source code
calculate_temperature_response_gaussian Man page Source code
calculate_temperature_response_johnson Man page Source code
calculate_temperature_response_polynomial Man page Source code
calculate_ternary_correction Man page Source code
calculate_total_pressure Man page Source code
calculate_wue Man page Source code
cbind.exdf Man page Source code
check_licor_data Man page Source code
check_optim_result Source code
check_optional_arguments Source code
check_required_variables Man page Source code
check_required_variables.data.frame Man page Source code
check_required_variables.exdf Man page Source code
check_response_curve_data Man page Source code
choose_input_files Man page Source code
choose_input_licor_files Man page Source code
choose_input_tdl_files Man page Source code
confidence_interval_all_param Source code
confidence_interval_one_param Source code
confidence_intervals_c3_aci Man page Source code
confidence_intervals_c3_variable_j Man page Source code
confidence_intervals_c4_aci Man page Source code
confidence_intervals_c4_aci_hyperbola Man page Source code
confidence_intervals_leaf_temperature Source code
consolidate Man page Source code
consolidate.data.frame Man page Source code
consolidate.exdf Man page Source code
constrain_guess Source code
control_regex_string Source code
conversions_from_text Source code
convert_param_setting Source code
csv.exdf Man page
debug_msg Source code
delta_13C Source code
deprecated Man page
dim.exdf Man page Source code
dimnames.exdf Man page Source code
dimnames<-.exdf Man page
document_variables Man page Source code
document_variables.data.frame Man page Source code
document_variables.exdf Man page Source code
error_function_c3_aci Man page Source code
error_function_c3_variable_j Man page Source code
error_function_c4_aci Man page Source code
error_function_c4_aci_hyperbola Man page Source code
estimate_licor_variance Man page Source code
estimate_operating_point Man page Source code
evaluate_polynomial Source code
example_data_files Man page
exclude_outliers Man page Source code
exclude_outliers.data.frame Man page Source code
exclude_outliers.exdf Man page Source code
exdf Man page Source code
extract.exdf Man page
extract_6800_excel_preamble_row Source code
extract_user_remark_table Source code
factorize_id_column Man page Source code
factorize_id_column.character Man page Source code
factorize_id_column.data.frame Man page Source code
factorize_id_column.exdf Man page Source code
fancy_column_names Source code
fit_ball_berry Man page Source code
fit_c3_aci Man page Source code
fit_c3_variable_j Man page Source code
fit_c4_aci Man page Source code
fit_c4_aci_hyperbola Man page Source code
fit_laisk Man page Source code
fit_medlyn Man page Source code
format_uc Source code
gaussian_response Source code
get_optional_argument Source code
get_oxygen_from_preamble Man page Source code
get_sample_valve_from_filename Man page Source code
identifier_columns Man page Source code
identifier_columns.data.frame Man page Source code
identifier_columns.exdf Man page Source code
identify_c3_limiting_processes Man page Source code
identify_c3_unreliable_points Source code
identify_c4_unreliable_points Source code
identify_common_columns Man page Source code
identify_common_columns.data.frame Man page Source code
identify_common_columns.exdf Man page Source code
identify_tdl_cycles Man page Source code
inform_user Source code
initial_guess_c3_aci Man page Source code
initial_guess_c3_variable_j Man page Source code
initial_guess_c4_aci Man page Source code
initial_guess_c4_aci_hyperbola Man page Source code
interpolate_assimilation_inputs Source code
is.exdf Man page Source code
jmax_error_msg Source code
jmax_from_j Source code
jmax_temperature_param_bernacchi Man page
jmax_temperature_param_flat Man page
johnson_eyring_williams Source code
length.exdf Man page Source code
licor_6800_lines_to_df Source code
licor_for_gm_site11 Man page
licor_for_gm_site11.xlsx Man page
licor_for_gm_site13 Man page
licor_for_gm_site13.xlsx Man page
multi_curve_colors Man page Source code
multi_curve_line_colors Man page Source code
multi_curve_point_colors Man page Source code
n_C3_A_limiting Source code
n_C4_A_smallest Source code
n_C4_V_smallest Source code
normalized_units Source code
optimizer_deoptim Man page Source code
optimizer_hjkb Man page Source code
optimizer_nlminb Man page Source code
optimizer_nmkb Man page Source code
optimizer_null Man page Source code
optimizers Man page
organize_response_curve_data Man page Source code
pair_gasex_and_tdl Man page Source code
pdf_print Man page Source code
photogea Man page
plaintext_licor_file Man page
plaintext_licor_file_v2 Man page
plot_ball_berry_fit Man page Source code
plot_c3_aci_fit Man page Source code
plot_c4_aci_fit Man page Source code
plot_c4_aci_hyperbola_fit Man page Source code
plot_laisk_fit Man page Source code
points_for_fitting Source code
print.exdf Man page Source code
process_6800_plaintext_header Source code
process_tdl_cycle_erml Man page Source code
process_tdl_cycle_polynomial Man page Source code
process_user_constant_rows_6800_excel Source code
process_user_constant_rows_6800_plaintext Source code
quadratic_root Source code
quadratic_root_max Source code
quadratic_root_min Source code
quadratic_root_minus Source code
quadratic_root_plus Source code
rbind.exdf Man page Source code
read.csv.exdf Man page Source code
read_cr3000 Man page Source code
read_gasex_file Man page Source code
read_licor_6800_Excel Man page Source code
read_licor_6800_plaintext Man page Source code
read_licor_file Man page Source code
read_tdl_file Man page Source code
remove_estimate Source code
remove_points Man page Source code
remove_repeated_colnames Source code
replace_unicode Source code
require_flexible_param Source code
require_optional_param Source code
residual_stats Man page Source code
set_column_info Source code
set_variable Man page Source code
smooth_tdl_data Man page Source code
split.exdf Man page Source code
standardize_gasex_columns Source code
str.exdf Man page Source code
tdl_for_gm Man page
tdl_for_gm.dat Man page
tdl_sampling_1 Man page
tdl_sampling_1.dat Man page
tdl_sampling_2 Man page
tdl_sampling_2.dat Man page
total_CO2 Source code
trust_value Source code
try_as_numeric Source code
unit_dictionary Source code
value_set Source code
write.csv.exdf Man page Source code
xyplot_avg_rc Man page Source code
PhotoGEA documentation built on Aug. 25, 2025, 5:13 p.m.

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