Changed fitting method from least-squares to maximum likelihood in fit_c3_aci, fit_c3_variable_j, and fit_c4_aci.
We use a normal distribution for calculating the likelihood.
Best-fit parameter values are determined with sigma = 1.
Then the true value of the likelihood can be estimated using sigma = RMSE.
Confidence intervals are also calculated using sigma = RMSE.
Fitting functions include the Akaike information criterion (AIC) in their outputs
Default settings have been changed to always calculate confidence intervals and remove unreliable parameter estimates, to use a more reliable (but slower) optimizer, and to fit alpha_old (for C3 A-Ci and Variable J fits); these settings will ensure more robust fitting results
Changed the C3 assimilation and Variable J equations to accommodate the new alpha parameters from Busch et al. (2018)
There are now three separate parameters: alpha_old (previously alpha_g), alpha_g, and alpha_s
If alpha_old is nonzero, then alpha_g and alpha_s must be zero. Likewise, if alpha_g or alpha_s is nonzero, then alpha_old must be zero. This will prevent users from mixing the two models together.
The fitting functions fit_c3_aci, fit_c3_variable_j, and fit_c4_aci now include a new output called fits_interpolated that contains values of the predicted assimilation rates with a Ci step of 1 ppm.
New plotting functions have been added: plot_c3_aci_fit and plot_c4_aci_fit. These functions use the new information in fits_interpolated to make nice plots comparing the measured data and the fits.
Now users can optionally ignore NA values when using xyplot_avg_rc and barchart_with_errorbars
Changed exclude_outliers to make sure it doesn’t exclude NA values
Specialized functions for writing exdf objects to CSV files and recreating exdf objects from those files are now available: write.csv.exdf and read.csv.exdf.
When determining the degree of trust in a best-fit parameter value, we now consider parameters with an upper confidence limit of Inf to be unreliable.
Light- and electron-limited assimilation has been added to calculate_c4_assimilation; now we have fully implemented the von Caemmerer model equations. This also necessitated a new function for temperature response calculations: calculate_peaked_gaussian.
New fitting parameters have been added to fit_c4_aci: alpha_psii, gbs, Jmax_at_opt and Rm_frac.
It is now possible to remove unreliable parameter estimates when using fit_c4_aci.
Tests have been updated to make sure the fitting functions can gracefully handle a fit failure, even when estimating confidence intervals and/or removing unreliable parameter estimates.
Added a new optimizer (optimizer_hjkb) and changed their default arguments so a user must always specify the tolerance or number of generations.
All functions that require an O2 partial pressure now calculate it from the total pressure and the oxygen concentration (expressed as a percentage).
A new option has been added to read_licor_6800_Excel and read_licor_6800_plaintext: get_oxygen. When this input is TRUE, get_oxygen_from_preamble will automatically be used to get the oxygen percentage from the file’s preamble when it is loaded.
A new option has been added to read_gasex_file: standardize_columns.
read_licor_6800_plaintext can now read log files that were closed and reopened
Added a new function called PhotoGEA_example_file_path to avoid using system.file in examples since system.path has been confusing for some users
check_licor_data has been renamed to check_response_curve_data since it is not limited to only Licor measurements
Specified a minimum supported R version: 3.6.0.
CHANGES IN PhotoGEA VERSION 0.11.0 (2024-02-12)
Added new options for adding penalties to the error function during Variable J fits, that enable the user to selectively penalize negative or unreasonably large values of mesophyll conductance.
Made a few improvements to C3 curve fitting functions (fit_c3_aci and fit_c3_variable_j):
Two more parameters can now be fit: alpha (related to TPU) and Gamma_star.
Unreliable parameter estimates can now be excluded; for example, if no points on a curve have An = Ap, the fit will return NA for TPU.
The initial guess functions (initial_guess_c3_aci and initial_guess_c3_variable_j) can now accommodate user-supplied values of alpha.
Made a few improvements to all three nonlinear fitting functions (fit_c3_aci, fit_c3_variable_j, and fit_c4_aci):
The error functions are now available in the package namespace as error_function_c3_aci, error_function_c3_variable_j, and error_function_c4_aci.
Confidence intervals around the best-fit values can now be calculated automatically by the fitting functions, or manually using three new functions in the package namespace: confidence_intervals_c3_aci, confidence_intervals_c3_variable_j, and confidence_intervals_c4_aci.
The initial guess functions are now created internally instead of being an input argument.
There is a new system for supplying fit options (upper and lower bounds, and which parameters to fit):
Users now only need to specify changes from the default settings.
The order of parameters no longer matters because lists of named elements are used.
Parameters that could be fit, but are not being fit, can either be set to fixed values or to values from a column of an exdf object.
Unknown parameters are now provided in alphabetical order when applicable (such as the first input arguments to calculate_c3_assimilation).
The functions are more tolerant to curves with severe problems (such as negative Ci) that prevent a good fit from being found; rather than throwing an error, the fit functions now silently return NA for all results, along with a message explaining the issue.
Added a function for estimating Rd with the Laisk method: calculate_rd_laisk
A “unit dictionary” was added for internal use; this may be expanded and used more often in the future.
Renamed several variables and input arguments:
Licor files contain a column called alpha, and several different “alphas” were used throughout PhotoGEA. To avoid confusion, the values in PhotoGEA were renamed as follows:
alpha_g: used in C3 assimilation calculations
alpha_pr: used in Gamma_star calculations
alpha_psii: used in C4 assimilation calculations
The acronym “TPU” was used to refer to a process (triose phosphate utilization) and the maximum rate of that process. To avoid confusion, the rate parameter was renamed to Tp
Tests were added for several functions:
calculate_c3_assimilation
fit_c3_aci
fit_c3_variable_j
fit_c4_aci
calculate_c3_limitations_grassi
calculate_c3_limitations_warren
The read_gasex_file function now automatically includes the filename as a column in the resulting exdf object; this helps with troubleshooting problematic curves or files.
Reorganized the variable J fitting functions to be more like fit_c3_aci:
Added calculate_c3_variable_j, initial_guess_c3_variable_j, and fit_c3_variable_j.
Removed dpmn_error_jrv, dpmn_error_jrvtt, dpmn_error_jrv_tau, dpmn_error_jrv_tpu, and photosynthesis_TRF.
Added a new optimizer from the DEoptim package (called optimizer_deoptim) and renamed default_optimizer to optimizer_nmkb. The new optimizer_deoptim is used as the default optimizer for variable J fitting.
Added two new functions for calculating the relative limiting factors of C3 photosynthesis: calculate_c3_limitations_grassi and calculate_c3_limitations_warren.
Added a new function for estimating the operating point from a measured A-Ci curve: estimate_operating_point.
Added two new color specifications (multi_curve_line_colors and multi_curve_point_colors) and used them in vignette examples.
fit_c3_aci and fit_c4_aci now use estimate_operating_point to automatically estimate the operating point and include it with the other fit parameters.
The C3 and C4 A-Ci vignettes now show include the operating point in one of the figures.
Renamed calculate_iwue to calculate_wue and provided documentation for this function, which now calculates two measures of leaf-level water use efficiency.
Provided documentation for factorize_id_columns and converted it to an S3 method so it can be applied to data frames and exdf objects.
Removed the process_id_column function since it can easily be replicated using paste.
Stopped reversing colors in xyplot_avg_rc.
Fixed a typo in calculate_c3_assimilation where Rd (the value of day respiration at 25 degrees C) was used in place of Rd_tl (the value of day respiration at the leaf temperature) when calculating net assimilation rates.
Added some developer documentation, an R CMD check GitHub workflow, and a code coverage GitHub workflow.
Added a new convenience function for printing plot objects: pdf_print
Added and/or documented several functions related to isotope discrimination measurements:
calculate_gamma_star
calculate_gm_busch
calculate_gm_ubierna
calculate_isotope_discrimination
calculate_leakiness_ubierna
calculate_ternary_correction
get_oxygen_from_preamble
get_sample_valve_from_filename
pair_gasex_and_tdl
Added two new example data files (licor_for_gm_site11.xslx and tdl_for_gm.dat) for use in examples and vignettes.
Renamed some variables related to isotope measurements; the new terms are more consistent with the way these quantities are typically described:
total_isotope_ratio was renamed to delta_13C
total_mixing_ratio was renamed to total_CO2
Removed a function that was specific to one user (batch_get_genotype_info_from_licor_filename).
Added a new R file (constants.R) to store the values of some constants that appear in multiple functions; this will help ensure that consistent values are used in each instance.
Improved some error handling in read_gasex_file and attempted to clarify instructions for selecting files to load.
Added two basic tests of read_gasex_file using the testthat package.
Modified identify_tdl_cycles and process_tdl_cycle_polynomial so they can handle cycles where there are multiple measurement logs from each valve.
Added several functions for calculating quadratic roots; these are not exported in the package namespace, but are now used in calculate_c3_assimilation and calculate_c4_assimilation to make the code cleaner and more robust.
Other updates to calculate_c3_assimilation:
Choose a minimal RuBP carboxylation rate rather than a minimal net CO2 assimilation rate.
Allow the user to specify a value of alpha (previously this value was hard-coded to 0).
Allow the user to specify two separate curvature values when including co-limitation.
Renamed min_aj_cutoff and max_aj_cutoff to cj_crossover_min and cj_crossover_max to better reflect their purpose.
Added new outputs from fit_c3_aci and fit_c4_aci that include the average values of leaf-temperature-dependent parameters like Vcmax and Rd.
Added options for specifying a flat temperature response when fitting C3 or C4 A-Ci curves; these are available via the two new data sets c3_arrhenius_no_temp and c4_arrhenius_no_temp.
plaintext_licor_file represents a plaintext Licor LI-6800 log file.
c4_aci_1.xlsx and c4_aci_2.xlsx contain examples of C4 A-Ci curves measured with Licor LI-6800 instruments.
Made several significant changes to functions that read data from log files:
Added the ability to read plaintext Licor LI-6800 log files.
Consolidated all file-reading functions into a single one called read_gasex_file.
Depending on user-supplied inputs that specify the instrument and file type, read_gasex_file internally calls either read_licor_6800_Excel, read_licor_6800_plaintext, or read_CR3000 to actually read the data from the file.
When loading LI-6800 Excel log files, it is no longer necessary to provide information about the preamble and data rows.
The previous reading functions read_licor_file and read_tdl_file are now deprecated. Since these functions are commonly used in scripts, a message will be sent to any users who attempt to call these functions. Eventually they will be completely removed from the package namespace.
Made significant changes to the way pressure values are handled:
Added a new function that calculates the total pressure inside a Licor chamber from the separate values of ambient pressure and the chamber overpressure: calculate_total_pressure.
Modified several other functions to just expect a value of total pressure rather than separate values of ambient pressure and chamber overpressure, since this system for storing pressure values is just an artifact of Licor log files:
apply_gm
calculate_c3_assimilation
calculate_gas_properties
fit_c3_aci
Renamed or modified several other functions:
calculate_cc is now apply_gm so it can be used for C3 and C4 photosynthesis calculations.
apply_gm was modified to include partial pressures in its outputs.
fit_c4_aci was modified to make it more like fit_c3_aci.
Added a new input argument to xyplot_avg_rc so that y-axis error bars can be disabled.
Added a new input argument to apply_gm so that drawdown calculations are now optional.
Improved some of the error messages generated by check_licor_data.
Included ATP and NADPH usage in the C3 assimilation calculations.
Added several other new functions:
initial_guess_c4_aci makes initial guesses for C4 photosynthetic parameters.
calculate_c4_assimilation calculates assimilation values using S. von Caemmerer’s model for C4 photosynthesis.
Added a new vignette demonstrating how to analyze C4 A-Ci curve data.
Modified fit_c3_aci so it now ensures that the initial guess lies within (and not on) the bounds. This is a requirement for the dfoptim::nmkb solver and presumably other bounded optimizers as well.
Moved the dfoptim package from Suggests to Imports because it is used by an essential part of PhotoGEA.
The check_required_variables function was moved to the package namespace.
Added and/or documented several functions:
A default optimizer function (default_optimizer).
A function for guessing for C3 parameter values (initial_guess_c3_aci).
A function for identifying columns that take a single unique value (identifier_columns).
A function that calculates error metrics from the values of residuals, including the root mean squared error (RMSE) and several others (residual_stats).
Small changes were made to several functions:
cbind.exdf no longer requires all objects to have the same number of rows.
[<-.exdf now allows users to remove columns by setting their values to NULL.
The conversion of the timestamp column to POSIXlt in read_tdl_file and read_licor_file can now be skipped by setting timestamp_colname to NA.
Significant changes have been made to fit_c3_aci:
It now has an option to set a curvature value that can be used to allow co-limitation of the net assimilation rate.
It now uses initial_guess_c3_aci to generate initial guesses by default.
It now has an option to fix certain parameter values (such as TPU) and exclude them from the fitting process via a new input argument called fixed.
Its output now includes residuals and error metrics such as the RMSE.
fit_ball_berry also returns residuals and error metrics in its output.
Two new vignettes were added:
“Creating Your Own Processing Tools” discusses the best practices for writing custom functions for processing. As an example, a function for fitting a rectangular hyperbola to an A-Ci curve is developed.
“Combining PhotoGEA With Other Packages” discusses best practices for writing wrappers for processing tools from other packages. As an example, a wrapper for plantecophys::fitaci is developed.
Several other vignettes were modified:
The “Analyzing C3 A-Ci Curves” vignette has been updated to include the new features of fit_c3_aci.
The “Developing a Data Analysis Pipeline” vignette has been updated to include the new functions added in this version.
The “Working With Extended Data Frames” vignette has been updated to include some new diagrams.
The “Getting Started With PhotoGEA” vignette has been updated to include links to the new vignettes.
Added a new vignette demonstrating how to analyze C3 A-Ci curve data.
Included TPU in the output from calculate_c3_assimilation.
In the organize_response_curve_data function, changed the default value of the ordering_column_tolerance column to Inf to disable this check by default, since we often want to reorder using a column like Ci that does not follow the same sequence of values in every curve.
Added new input arguments to fit_c3_aci: min_aj_cutoff and max_aj_cutoff, which provide a way to constrain the range of Cc where Aj is allowed to be the limiting assimilation rate.
Added new function for calibrating TDL data (process_tdl_cycle_polynomial) and an option for using it in the gm_from_tdl script.
Modified Licor-TDL pairing to stop assuming a particular relationship between the sample and reference valve numbers.
Fixed an issue with calculate_c3_assimilation that was causing it to report incorrect An values at low Cc.
Fixed several typos where Ac was misidentified as the “RuBP-limited” rate; in fact, it is the RuBP-saturated rate but is more commonly referred to as the rubisco-limited rate.
This version adds a substantial amount of documentation, including a vignette describing how to use PhotoGEA to analyze TDL data.
While working on documentation, several changes were made to key functions so they behaved more reasonably and became easier to document.
Changes to functions and their documentation includes:
exdf objects can now be initialized from just a data frame; in this case, units and categories will all be NA.
apply_fit_across_reps and process_tdl_cycles have been replaced by two new lower-level functions that offer more generality: by.exdf and consolidate.
check_response_curve_data and check_signal_averaging_data have been consolidated into one function: check_licor_data.
An exdf method for cbind has been added.
exclude_tdl_cycles and extract_tdl_valve have been removed since they can easily be reproduced with more basic exdf functionality.
All functions for creating or modifying Excel files have been removed since we no longer want to follow this strategy.
basic_stats and the “Variable J” example script have been fixed.
CHANGES IN PhotoGEA VERSION 0.2.0 (2022-07-26)
This version adds a substantial amount of documentation, including a vignette describing how to use PhotoGEA to analyze Ball-Berry data.
While working on documentation, several changes were made to key functions so they behaved more reasonably and became easier to document.
At the moment, basic_stats and the “Variable J” example script have been broken.
CHANGES IN PhotoGEA VERSION 0.1.0
This is the first version of PhotoGEA. At this point, the package is in a state of rapid development, and not all changes will be described here.
We are reserving version 1.0.0 for the first version where all R package functions and data sets have been documented; until then, major changes should only increase the minor version number.
