Release v0.11.0

[eloch216]

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 accomodate 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.
• PRs related to creating this version:
  • https://github.com/eloch216/PhotoGEA/pull/85
  • https://github.com/eloch216/PhotoGEA/pull/86
  • https://github.com/eloch216/PhotoGEA/pull/88
  • https://github.com/eloch216/PhotoGEA/pull/89

[codecov[bot]]

Codecov Report

Attention: 117 lines in your changes are missing coverage. Please review.

Comparison is base (9b59a28) 85.42% compared to head (9af5f81) 86.11%. Report is 4 commits behind head on main.

Files	Patch %	Lines
R/confidence_intervals_c3_variable_j.R	0.00%	34 Missing :warning:
R/fit_c3_variable_j.R	85.71%	27 Missing :warning:
R/error_function_c3_variable_j.R	87.82%	14 Missing :warning:
R/calculate_c4_assimilation.R	76.92%	12 Missing :warning:
R/calculate_c3_assimilation.R	89.55%	7 Missing :warning:
R/calculate_c3_variable_j.R	78.78%	7 Missing :warning:
R/remove_C3_unreliable_points.R	75.86%	7 Missing :warning:
R/confidence_intervals.R	96.42%	2 Missing :warning:
R/calculate_rd_laisk.R	98.30%	1 Missing :warning:
R/confidence_intervals_c3_aci.R	96.66%	1 Missing :warning:
... and 5 more

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #89 +/- ## ========================================== + Coverage 85.42% 86.11% +0.69% ========================================== Files 64 74 +10 Lines 3018 3717 +699 ========================================== + Hits 2578 3201 +623 - Misses 440 516 +76 ```

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