Files in PhotoGEA

Photosynthetic Gas Exchange Analysis

NEWS.md README.md R/confidence_intervals_c4_aci_hyperbola.R R/error_function_c3_aci.R R/fit_medlyn.R R/unicode_replacements.R R/read_cr3000.R R/calculate_isotope_discrimination.R R/confidence_intervals_c3_variable_j.R R/apply_gm.R R/identify_unreliable_points.R R/calculate_gas_properties.R R/plot_c4_aci_fit.R R/fit_c4_aci.R R/calculate_c4_assimilation.R R/calculate_c3_variable_j.R R/residual_stats.R R/PhotoGEA_example_file_path.R R/unit_dictionary.R R/consolidate.R R/fit_helping_functions.R R/initial_guess_c3_aci.R R/calculate_temperature_response_polynomial.R R/confidence_intervals.R R/check_required_variables.R R/quadratic_roots.R R/basic_stats.R R/multi_curve_colors.R R/choose_input_tdl_files.R R/initial_guess_c4_aci.R R/plot_laisk_fit.R R/read_licor_6800_Excel.R R/interpolate_assimilation_inputs.R R/identify_C4_unreliable_points.R R/fit_c3_aci.R R/initial_guess_c3_variable_j.R R/calculate_jmax.R R/standardize_gasex_columns.R R/deprecated.R R/choose_input_licor_files.R R/get_sample_valve_from_filename.R R/calculate_gm_ubierna.R R/A_limiting.R R/calculate_c3_assimilation.R R/error_function_c4_aci_hyperbola.R R/calculate_ball_berry_index.R R/calculate_wue.R R/fit_c3_variable_j.R R/identify_common_columns.R R/identify_C3_unreliable_points.R R/estimate_operating_point.R R/organize_response_curve_data.R R/pdf_print.R R/error_penalty.R R/process_tdl_cycle_polynomial.R R/optimizers.R R/factorize_id_column.R R/get_optional_argument.R R/plot_c4_aci_hyperbola_fit.R R/calculate_leakiness_ubierna.R R/calculate_temperature_response.R R/calculate_temperature_response_arrhenius.R R/calculate_ternary_correction.R R/calculate_gamma_star.R R/bwplot_wrapper.R R/remove_repeated_colnames.R R/try_as_numeric.R R/fit_c4_aci_hyperbola.R R/error_function_c4_aci.R R/pair_gasex_and_tdl.R R/read_licor_6800_plaintext.R R/read_gasex_file.R R/estimate_licor_variance.R R/error_function_c3_variable_j.R R/identify_c3_limiting_processes.R R/calculate_temperature_response_gaussian.R R/initial_guess_c4_aci_hyperbola.R R/remove_points.R R/set_variable.R R/exclude_outliers.R R/check_optional_arguments.R R/constants.R R/calculate_residuals.R R/identifier_columns.R R/barchart_with_errorbars.R R/check_response_curve_data.R R/calculate_gm_busch.R R/calculate_c4_assimilation_hyperbola.R R/fit_ball_berry.R R/calculate_c3_limitations_grassi.R R/exdf.R R/points_for_fitting.R R/fit_laisk.R R/process_tdl_cycle.R R/plot_ball_berry_fit.R R/get_oxygen_from_preamble.R R/identify_tdl_cycles.R R/confidence_intervals_c3_aci.R R/process_tdl_cycle_erml.R R/calculate_temperature_response_johnson.R R/xyplot_avg_rc.R R/calculate_total_pressure.R R/confidence_intervals_c4_aci.R R/smooth_tdl_data.R R/calculate_c3_limitations_warren.R R/document_variables.R R/plot_c3_aci_fit.R R/choose_input_files.R inst/doc/PhotoGEA.R inst/doc/PhotoGEA.Rmd tests/testthat.R tests/testthat/test-assemble_luf.R tests/testthat/test-check_response_curve_data.R tests/testthat/test-calculate_c3_limitations_grassi.R tests/testthat/test-optimizers.R tests/testthat/test-fit_medlyn.R tests/testthat/test-fit_laisk.R tests/testthat/test-PhotoGEA_example_file_path.R tests/testthat/test-exdf.R tests/testthat/test-calculate_residuals.R tests/testthat/test-estimate_operating_point.R tests/testthat/test-unit_dictionary.R tests/testthat/test-exclude_outliers.R tests/testthat/test-read_licor_6800_plaintext.R tests/testthat/test-calculate_ball_berry_index.R tests/testthat/test-calculate_temperature_response.R tests/testthat/test-set_variable.R tests/testthat/get_duplicated_colnames.R tests/testthat/test-deprecated.R tests/testthat/test-residual_stats.R tests/testthat/test-identifier_columns.R tests/testthat/test-basic_stats.R tests/testthat/test-fit_c4_aci_hyperbola.R tests/testthat/one_curve_c3_aci.R tests/testthat/test-rbind.exdf.R tests/testthat/test-document_variables.R tests/testthat/test-fit_c4_aci.R tests/testthat/test-read.csv.exdf.R tests/testthat/test-calculate_c4_assimilation_hyperbola.R tests/testthat/test-calculate_c3_limitations_warren.R tests/testthat/one_curve_ball_berry.R tests/testthat/one_curve_c4_aci.R tests/testthat/test-organize_response_curve_data.R tests/testthat/test-read_gasex_file.R tests/testthat/test-read_licor_6800_Excel.R tests/testthat/test-fit_c3_variable_j.R tests/testthat/test-calculate_c3_assimilation.R tests/testthat/test-fit_c3_aci.R tests/testthat/test-barchart_with_errorbars.R tests/testthat/test-fit_ball_berry.R tests/testthat/test-check_required_variables.R tests/testthat/test-identify_c3_limiting_processes.R tests/testthat/test-factorize_id_column.R tests/testthat/test-calculate_c4_assimilation.R vignettes/PhotoGEA.Rmd data/c3_temperature_param_flat.R data/jmax_temperature_param_bernacchi.R data/c3_temperature_param_bernacchi.R data/c4_temperature_param_vc.R data/c4_temperature_param_flat.R data/jmax_temperature_param_flat.R data/c3_temperature_param_sharkey.R man/fit_c4_aci.Rd man/apply_gm.Rd man/organize_response_curve_data.Rd man/identifier_columns.Rd man/confidence_intervals_c4_aci_hyperbola.Rd man/calculate_gm_ubierna.Rd man/check_response_curve_data.Rd man/calculate_temperature_response_polynomial.Rd man/read_licor_6800_plaintext.Rd man/c3_temperature_param_sharkey.Rd man/plot_laisk_fit.Rd man/consolidate.Rd man/error_function_c3_variable_j.Rd man/get_sample_valve_from_filename.Rd man/jmax_temperature_param_bernacchi.Rd man/calculate_temperature_response_arrhenius.Rd man/calculate_gm_busch.Rd man/calculate_c3_assimilation.Rd man/choose_input_files.Rd man/dimnames.exdf.Rd man/calculate_temperature_response.Rd man/plot_ball_berry_fit.Rd man/str.exdf.Rd man/length.exdf.Rd man/by.exdf.Rd man/example_data_files.Rd man/xyplot_avg_rc.Rd man/PhotoGEA_example_file_path.Rd man/calculate_gas_properties.Rd man/estimate_operating_point.Rd man/pdf_print.Rd man/calculate_c4_assimilation.Rd man/calculate_c3_limitations_warren.Rd man/optimizers.Rd man/fit_laisk.Rd man/is.exdf.Rd man/exdf.Rd man/identify_common_columns.Rd man/c3_temperature_param_bernacchi.Rd man/plot_c4_aci_fit.Rd man/identify_tdl_cycles.Rd man/estimate_licor_variance.Rd man/extract.exdf.Rd man/read_licor_6800_Excel.Rd man/calculate_gamma_star.Rd man/exclude_outliers.Rd man/c4_temperature_param_vc.Rd man/fit_c3_aci.Rd man/pair_gasex_and_tdl.Rd man/calculate_isotope_discrimination.Rd man/calculate_ternary_correction.Rd man/PhotoGEA.Rd man/process_tdl_cycle_polynomial.Rd man/print.exdf.Rd man/split.exdf.Rd man/fit_medlyn.Rd man/fit_ball_berry.Rd man/read_gasex_file.Rd man/initial_guess_c4_aci.Rd man/calculate_total_pressure.Rd man/calculate_jmax.Rd man/smooth_tdl_data.Rd man/error_function_c4_aci.Rd man/identify_c3_limiting_processes.Rd man/plot_c4_aci_hyperbola_fit.Rd man/jmax_temperature_param_flat.Rd man/process_tdl_cycle_erml.Rd man/c4_temperature_param_flat.Rd man/fit_c4_aci_hyperbola.Rd man/fit_c3_variable_j.Rd man/error_function_c4_aci_hyperbola.Rd man/initial_guess_c4_aci_hyperbola.Rd man/dim.exdf.Rd man/confidence_intervals_c3_variable_j.Rd man/calculate_c4_assimilation_hyperbola.Rd man/calculate_leakiness_ubierna.Rd man/read_cr3000.Rd man/get_oxygen_from_preamble.Rd man/deprecated.Rd man/confidence_intervals_c3_aci.Rd man/document_variables.Rd man/multi_curve_colors.Rd man/plot_c3_aci_fit.Rd man/calculate_wue.Rd man/remove_points.Rd man/calculate_c3_variable_j.Rd man/initial_guess_c3_aci.Rd man/calculate_c3_limitations_grassi.Rd man/calculate_temperature_response_johnson.Rd man/confidence_intervals_c4_aci.Rd man/c3_temperature_param_flat.Rd man/calculate_temperature_response_gaussian.Rd man/error_function_c3_aci.Rd man/factorize_id_column.Rd man/barchart_with_errorbars.Rd man/check_required_variables.Rd man/set_variable.Rd man/residual_stats.Rd man/as.data.frame.exdf.Rd man/cbind.exdf.Rd man/basic_stats.Rd man/calculate_ball_berry_index.Rd man/csv.exdf.Rd man/initial_guess_c3_variable_j.Rd