Package index
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PhotoGEA_example_file_path()
- Locate a PhotoGEA example file on your computer
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apply_gm()
- Calculate CO2 concentration in the chloroplast or mesophyll
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as.data.frame(<exdf>)
- Convert an exdf object to a data frame
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barchart_with_errorbars()
bwplot_wrapper()
- Barcharts with error bars
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basic_stats()
- Calculate basic stats (mean and standard error)
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by(<exdf>)
- Apply a function to an exdf object split by one or more factors
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c3_arrhenius_bernacchi
- C3 Arrhenius parameters from Bernacchi et al.
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c3_arrhenius_no_temp
- C3 Arrhenius parameters with no temperature dependence
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c3_arrhenius_sharkey
- C3 Arrhenius parameters from Sharkey et al.
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c4_arrhenius_no_temp
- C4 Arrhenius parameters with no temperature dependence
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c4_arrhenius_von_caemmerer
- C4 Arrhenius parameters from von Caemmerer
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c4_peaked_gaussian_no_temp
- C4 peaked Gaussian parameters with no temperature response
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c4_peaked_gaussian_von_caemmerer
- C4 Arrhenius parameters from von Caemmerer
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calculate_RL_laisk()
- Calculate RL using the Laisk method
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calculate_arrhenius()
- Calculate temperature-dependent values using Arrhenius equations
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calculate_ball_berry_index()
- Calculate the Ball-Berry index
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calculate_c3_assimilation()
- Calculate C3 assimilation rates
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calculate_c3_limitations_grassi()
- Estimate the relative limiting factors to C3 photosynthesis
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calculate_c3_limitations_warren()
- Estimate the relative limiting factors to C3 photosynthesis
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calculate_c3_variable_j()
- Calculate C3 variable J
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calculate_c4_assimilation()
- Calculate C4 assimilation rates
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calculate_c4_assimilation_hyperbola()
- Calculate C4 assimilation rates using a hyperbola
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calculate_gamma_star()
- Calculate Gamma_star from Rubisco specificity
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calculate_gas_properties()
- Calculate gas properties that are typically not included in Licor files
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calculate_gm_busch()
- Calculate mesophyll conductance to CO2 diffusion
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calculate_gm_ubierna()
- Calculate mesophyll conductance to CO2 diffusion
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calculate_isotope_discrimination()
- Calculate photosynthetic isotope discrimination
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calculate_leakiness_ubierna()
- Calculate leakiness
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calculate_peaked_gaussian()
- Calculate temperature-dependent values using Gaussian equations
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calculate_ternary_correction()
- Calculate ternary correction factor
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calculate_total_pressure()
- Calculate the total pressure in bar
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calculate_wue()
- Calculate intrinsic water use efficiency
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cbind(<exdf>)
rbind(<exdf>)
- Combine exdf objects by columns or rows
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check_required_variables()
- Make sure required variables exist
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check_response_curve_data()
- Check response curve data for common issues
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choose_input_files()
choose_input_licor_files()
choose_input_tdl_files()
- Choosing input files
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confidence_intervals_c3_aci()
- Calculate confidence intervals for C3 A-Ci fitting parameters
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confidence_intervals_c3_variable_j()
- Calculate confidence intervals for C3 Variable J fitting parameters
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confidence_intervals_c4_aci()
- Calculate confidence intervals for C4 A-Ci fitting parameters
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confidence_intervals_c4_aci_hyperbola()
- Calculate confidence intervals for C4 A-Ci hyperbola fitting parameters
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consolidate()
- Consolidate a list of lists
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read.csv.exdf()
write.csv.exdf()
- Read and write CSV files representing an exdf object
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read_tdl_file()
read_licor_file()
check_licor_data()
- Deprecated functions
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dim(<exdf>)
- Retrieve the dimension of an exdf object
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dimnames(<exdf>)
`dimnames<-`(<exdf>)
- Retrieve or set the dimension names of an exdf object
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document_variables()
- Document exdf columns by specifying units and categories
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error_function_c3_aci()
- Generate an error function for C3 A-Ci curve fitting
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error_function_c3_variable_j()
- Generate an error function for C3 Variable J curve fitting
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error_function_c4_aci()
- Generate an error function for C4 A-Ci curve fitting
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error_function_c4_aci_hyperbola()
- Generate an error function for C4 A-Ci curve fitting with a hyperbola
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estimate_licor_variance()
- Estimate variance of measured Licor values
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estimate_operating_point()
- Estimate the operating point from an A-Ci curve
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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
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exclude_outliers()
- Exclude outliers from a data set
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exdf()
- Extended data frame
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`[`(<exdf>)
`[<-`(<exdf>)
- Access or modify exdf elements
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factorize_id_column()
- Convert ID column to a factor with a suitable ordering
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fit_ball_berry()
- Fits the Ball-Berry model to an experimental curve
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fit_c3_aci()
- Fits a C3 assimilation model to an experimental curve
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fit_c3_variable_j()
- Fits a C3 assimilation model to an experimental curve
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fit_c4_aci()
- Fits a C4 assimilation model to an experimental curve
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fit_c4_aci_hyperbola()
- Fits a hyperbolic C4 assimilation model to an experimental curve
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get_oxygen_from_preamble()
- Extract oxygen information from a Licor file
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get_sample_valve_from_filename()
- Extract TDL valve information from file name
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identifier_columns()
- Find columns that have a single value across all rows
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identify_common_columns()
- Identify columns that are common to multiple objects
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identify_tdl_cycles()
- Identifying cycles in TDL data
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initial_guess_c3_aci()
- Make an initial guess of FvCB model parameter values for one curve
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initial_guess_c3_variable_j()
- Make an initial guess of "variable J" model parameter values for one curve
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initial_guess_c4_aci()
- Make an initial guess of C4 photosynthesis parameter values for one curve
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initial_guess_c4_aci_hyperbola()
- Make an initial guess of C4 hyperbola parameter values for one curve
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is.exdf()
- Is an object an exdf?
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length(<exdf>)
- Length of an exdf object
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multi_curve_colors()
multi_curve_line_colors()
multi_curve_point_colors()
- Set of colors for plotting multiple curves
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optimizer_nmkb()
optimizer_hjkb()
optimizer_deoptim()
- Optimizers
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organize_response_curve_data()
- Reorganize response curve data for analysis and plotting
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pair_gasex_and_tdl()
- Pair gas exchange and TDL data
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pdf_print()
- Print a plot object or save it to a PDF
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plot_c3_aci_fit()
- Plot the results of a C3 CO2 response curve fit
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plot_c4_aci_fit()
- Plot the results of a C4 CO2 response curve fit
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plot_c4_aci_hyperbola_fit()
- Plot the results of a hyperbolic C4 CO2 response curve fit
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print(<exdf>)
- Print the contents of an exdf object
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process_tdl_cycle_erml()
- Process cycles from the ERML TDL
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process_tdl_cycle_polynomial()
- Process TDL cycles using a polynomial correction method
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read_cr3000()
- Reading a CR3000 data file
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read_gasex_file()
- Reading a gas exchange log file
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read_licor_6800_Excel()
- Reading a Licor LI-6800 Excel log file
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read_licor_6800_plaintext()
- Reading a Licor LI-6800 plaintext log file
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remove_points()
- Remove specific points from an exdf object
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residual_stats()
- Calculate statistics that describe the residuals of a fit
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set_variable()
- Document exdf columns by specifying units and categories
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smooth_tdl_data()
- Smoothing data from one TDL valve
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split(<exdf>)
- Divide an exdf object into groups
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str(<exdf>)
- Display the structure of an exdf object
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xyplot_avg_rc()
- Plot average response curves with error bars