Update Trial Planning Vignette

[holgstr]

Refactoring trial planning vignette:

• a few sentences are rephrased to match wording of new functions
• changes name of powerEmp to empSignificant

[holgstr]

Dear @danielinteractive, I decided to reproduce scenario 2 from the paper for the vignette. However, I cannot reproduce the required OS sample size according to Schoenfeld (732 in the vignette, 708 in the paper). See also the sample code in the linked issue opened by Kaspar.

[github-actions]

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ---------
R/assertions.R                  15       0  100.00%
R/empSignificant.R              59       0  100.00%
R/eventTracking.R               88       2  97.73%   48, 244
R/getClinicalTrials.R           64       0  100.00%
R/getSimulatedData.R           107       0  100.00%
R/getWaitTimeSum.R              29       2  93.10%   45, 48
R/hazardFunctions.R             26       0  100.00%
R/piecewiseDistribution.R       32       0  100.00%
R/piecewiseHazards.R            18       0  100.00%
R/survivalFunctions.R           96       0  100.00%
R/transitionParameters.R        42       0  100.00%
TOTAL                          576       4  99.31%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/empSignificant.R             +59       0  +100.00%
R/eventTracking.R               +8       0  +0.23%
R/getClinicalTrials.R           +6       0  +100.00%
R/getSimulatedData.R            +5       0  +100.00%
R/hazardFunctions.R            +26       0  +100.00%
R/piecewiseDistribution.R       -1       0  +100.00%
R/piecewiseHazards.R            +1       0  +100.00%
R/survivalFunctions.R          +96       0  +100.00%
TOTAL                         +200       0  +0.37%

Results for commit: 0b049b0

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[danielinteractive]

Interesting thanks @holgstr , so is there now new content in the vignette? Or just refactored? I would go first for pure refactoring and then in separate PR add new content.

[holgstr]

Hm, I guess I might have misunderstood what „refactoring“ means? 😄 I have substituted the R code with the newly added functions, renamed the powerEmp function to empSignificance, and along the way rephrased some sentences in the vignette to match the wording of the package/functions better. The only truly new content is the small chunk in the vignette where sample sizes are calculated according to Schoenfeld via rpact. I now see you may prefer me to break up the PR into two smaller ones? Should I do this now or rather keep it in mind going forward?

[danielinteractive]

I would say the problematic part of it is new where you cannot reproduce the paper let's split this into separate PR.

[danielinteractive]

Sorry about the confusion Kaspars issue refers to the new addition, let's keep this PR to the refactoring I.e. using the new functions you added etc

[holgstr]

I have left out the addition of computing the sample sizes via Schoenfeld, so this PR now includes only refactoring + renaming powerEmp to empSignificant.

[github-actions]

Unit Tests Summary

    1 files    14 suites   2m 26s ⏱️
  57 tests   57 ✔️ 0 💤 0 ❌
138 runs  138 ✔️ 0 💤 0 ❌

Results for commit 0b6096c.