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Implements the Brier Score #241

Merged
merged 6 commits into from
Nov 7, 2023
Merged

Implements the Brier Score #241

merged 6 commits into from
Nov 7, 2023

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gowerc
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@gowerc gowerc commented Nov 2, 2023

Closes #7

@danielinteractive danielinteractive self-assigned this Nov 2, 2023
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github-actions bot commented Nov 2, 2023

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Code Coverage Summary

Filename                       Stmts    Miss  Cover    Missing
---------------------------  -------  ------  -------  ----------------------
R/brier_score.R                  166       0  100.00%
R/DataJoint.R                     76       2  97.37%   264, 270
R/DataLongitudinal.R             119       1  99.16%   245
R/DataSubject.R                   69       1  98.55%   124
R/DataSurvival.R                  74       1  98.65%   146
R/defaults.R                      13       7  46.15%   27, 45-84, 111
R/generics.R                      16       1  93.75%   69
R/JointModel.R                    91       8  91.21%   113-125, 204, 210, 216
R/JointModelSamples.R             54       0  100.00%
R/Link.R                          18       0  100.00%
R/LinkGSF.R                       69      13  81.16%   116-128
R/LinkNone.R                       5       1  80.00%   36
R/LinkRandomSlope.R               11       0  100.00%
R/LongitudinalGSF.R               24       0  100.00%
R/LongitudinalModel.R             17       0  100.00%
R/LongitudinalQuantities.R        85       8  90.59%   100-107
R/LongitudinalRandomSlope.R       22       0  100.00%
R/Parameter.R                     14       0  100.00%
R/ParameterList.R                 37       1  97.30%   175
R/Prior.R                        117       0  100.00%
R/Quantities.R                   105       0  100.00%
R/simulations_gsf.R               43       0  100.00%
R/simulations_os.R                11       5  54.55%   35-39
R/simulations_rs.R                21       0  100.00%
R/simulations.R                   99       1  98.99%   122
R/StanModel.R                     14       0  100.00%
R/StanModule.R                   158       4  97.47%   197-198, 240, 251
R/SurvivalExponential.R           10       0  100.00%
R/SurvivalLoglogistic.R           11       0  100.00%
R/SurvivalModel.R                 19       0  100.00%
R/SurvivalQuantities.R           151       6  96.03%   173-178
R/SurvivalWeibullPH.R             11       0  100.00%
R/utilities.R                    145       1  99.31%   13
R/zzz.R                           11      11  0.00%    4-29
TOTAL                           1906      72  96.22%

Diff against main

Filename                  Stmts    Miss  Cover
----------------------  -------  ------  --------
R/brier_score.R            +166       0  +100.00%
R/generics.R                 +1       0  +0.42%
R/SurvivalQuantities.R      +32       0  +1.07%
TOTAL                      +199       0  +0.44%

Results for commit: 5159392

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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@danielinteractive danielinteractive left a comment

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Thank you @gowerc , looks very nice!

I wonder if it would be possible to add a methods details vignette where you describe the Brier Score calculations? That would make it easier for future developers before jumping into the code

R/SurvivalQuantities.R Outdated Show resolved Hide resolved
R/brier_score.R Outdated Show resolved Hide resolved
R/brier_score.R Show resolved Hide resolved
R/brier_score.R Outdated Show resolved Hide resolved
tests/testthat/test-brierScore.R Outdated Show resolved Hide resolved
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github-actions bot commented Nov 2, 2023

Unit Tests Summary

    1 files    34 suites   2m 59s ⏱️
  92 tests   68 ✔️ 24 💤 0
306 runs  282 ✔️ 24 💤 0

Results for commit 5159392.

♻️ This comment has been updated with latest results.

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gowerc commented Nov 6, 2023

@danielinteractive - I think I addressed your review comments, I added an additional outline of the "Brier Score" in a statistical specification Rmd file. Please take a look and let me know if you have any comments

@danielinteractive danielinteractive self-requested a review November 6, 2023 19:27
@gowerc gowerc merged commit b4957b2 into main Nov 7, 2023
23 checks passed
@gowerc gowerc deleted the feature/brier_score branch November 7, 2023 12:16
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Implement scaled Brier Derivation
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