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More tweaks #88

Merged
merged 11 commits into from
Feb 12, 2024
Merged

More tweaks #88

merged 11 commits into from
Feb 12, 2024

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eloch216
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This PR adds new options for constraining the optimizer during Variable J fits, and makes several other "quality of life" updates

Added tests for the Warren function

Renamed the `alpha` used in TPU calculations because there is a Licor column called `alpha`

`check_required_variables` no longer throws an error if a column is NA
Rename alpha used for calculating Gamma_star

Rename alpha used in C4 assimilation
Now we can distinguish between the process (triose phosphate utilization; TPU) and the maximum rate at which the process occurs (Tp)
@eloch216 eloch216 changed the base branch from main to unreleased February 12, 2024 21:43
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codecov bot commented Feb 12, 2024

Codecov Report

Attention: 32 lines in your changes are missing coverage. Please review.

Comparison is base (0468c79) 85.17% compared to head (cd9b410) 86.11%.
Report is 4 commits behind head on unreleased.

Files Patch % Lines
R/calculate_c4_assimilation.R 73.33% 8 Missing ⚠️
R/calculate_c3_assimilation.R 82.05% 7 Missing ⚠️
R/error_function_c3_variable_j.R 68.42% 6 Missing ⚠️
R/calculate_c3_variable_j.R 75.00% 5 Missing ⚠️
R/confidence_intervals_c3_variable_j.R 0.00% 3 Missing ⚠️
R/fit_c3_variable_j.R 96.29% 3 Missing ⚠️
Additional details and impacted files
@@              Coverage Diff               @@
##           unreleased      #88      +/-   ##
==============================================
+ Coverage       85.17%   86.11%   +0.93%     
==============================================
  Files              74       74              
  Lines            3657     3717      +60     
==============================================
+ Hits             3115     3201      +86     
+ Misses            542      516      -26     

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@eloch216 eloch216 merged commit 8f9ae23 into unreleased Feb 12, 2024
9 checks passed
@eloch216 eloch216 deleted the more-tweaks branch February 12, 2024 21:59
@eloch216 eloch216 mentioned this pull request Feb 12, 2024
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