corPFSOS

[holgstr]

Fixes #90

[holgstr]

@danielinteractive this is the draft for the corPFSOS function, without docu & tests :)

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
getSimulatedDataDistib	💔	$95.65$	$+1.87$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
getSimulatedDataDistib	💔	$49.72$	$+1.99$	getSimulatedData_generates_distributions_as_expected_Weibull

Results for commit c3401c7

♻️ This comment has been updated with latest results.

[danielinteractive]

thanks @holgstr , nice work, please see for suggested next steps below

[github-actions]

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  -----------
R/assertions.R                  15       0  100.00%
R/corPFSOS.R                    68      68  0.00%    14-300
R/empSignificant.R              59       0  100.00%
R/estimateParams.R              75       5  93.33%   35, 138-141
R/eventTracking.R               88       2  97.73%   48, 244
R/getClinicalTrials.R           71       0  100.00%
R/getSimulatedData.R           109       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          111       0  100.00%
R/transitionParameters.R        42       0  100.00%
TOTAL                          743      77  89.64%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  --------
R/corPFSOS.R            +68     +68  +100.00%
R/estimateParams.R       +4      +4  -5.26%
TOTAL                   +72     +72  -9.62%

Results for commit: 2505e0d

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    15 suites   2m 12s ⏱️
  80 tests   79 ✔️ 1 💤 0 ❌
184 runs  183 ✔️ 1 💤 0 ❌

Results for commit 6bd2761.

♻️ This comment has been updated with latest results.

[holgstr]

@danielinteractive I have now documented all the functions. The main functions are:

• corTrans(transition) computes the correlation for a given transition with parameters stored inside
• corPFSOS(data, transition, boostrap = TRUE) estimates correlation for a given data set and distribution assumed via transition. I have also included a prototype bootstrap procedure inside, but this uses a for-loop. We would probably want to speed this up, so I thought about parallelization. Is there any good package/way of doing this you could recommend?

[danielinteractive]

Thanks @holgstr , let's please separate out the bootstrap part in a new issue and PR. You can still add the corPFSOS function but still without the bootstrap here

[danielinteractive]

is this the way the survival bootstrap works? see Kaspar's reference