96 bounds predprob #105

audreyyeoCH · 2024-05-26T17:51:36Z

closes #96

github-actions · 2024-05-26T18:08:20Z

Code Coverage Summary

Filename                 Stmts    Miss  Cover    Missing
---------------------  -------  ------  -------  ----------------------------------
R/betadiff.R                59       0  100.00%
R/boundsPostprob.R          44       0  100.00%
R/boundsPredprob.R          53       1  98.11%   77
R/dbetabinom.R              81       3  96.30%   32, 62, 136
R/oc2.R                    162     162  0.00%    93-326
R/oc3.R                    146     146  0.00%    91-308
R/ocPostprob.R              99       4  95.96%   239-242
R/ocPostprobDist.R         109       0  100.00%
R/ocPredprob.R             182       4  97.80%   285-288
R/ocPredprobDist.R         235       3  98.72%   346-348
R/ocRctPostprobDist.R      154       4  97.40%   236-239
R/ocRctPredprobDist.R      283      55  80.57%   207-222, 225-240, 373-376, 403-421
R/plotBeta.R               103      90  12.62%   60-167
R/plotBounds.R              52      52  0.00%    33-90
R/plotDecision.R            79      79  0.00%    16-136
R/plotOc.R                  15      15  0.00%    16-36
R/postprob.R                34       1  97.06%   106
R/postprobDist.R            77       1  98.70%   204
R/predprob.R                24       0  100.00%
R/predprobDist.R           140       1  99.29%   269
R/runShinyPhase1b.R          4       4  0.00%    8-13
R/sumbetadiff.R             63      63  0.00%    24-101
R/sumTable.R                20      20  0.00%    25-48
TOTAL                     2218     708  68.08%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/boundsPredprob.R      +25     -27  +98.11%
R/predprobDist.R         -1       0  -0.01%
TOTAL                   +24     -27  +1.58%

Results for commit: c661bdf

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2024-05-26T20:47:38Z

Unit Tests Summary

1 files 15 suites 1m 50s ⏱️
119 tests 119 ✅ 0 💤 0 ❌
1 266 runs 1 266 ✅ 0 💤 0 ❌

Results for commit 258ae08.

♻️ This comment has been updated with latest results.

github-actions · 2024-05-26T20:47:41Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
boundsPredprob	👶		$+0.18$	$+18$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
boundsPredprob	👶		$+0.13$	boundsPredprob_gives_correct_result_and_when_default_weight_is_not_assigned
boundsPredprob	👶		$+0.05$	boundsPredprob_with_Beta_Mixture_Priors_give_correct_results

Results for commit 5aed66e

♻️ This comment has been updated with latest results.

audreyyeoCH · 2024-10-07T21:36:22Z

I found some test cases failing and am working on it before I feel confident to request PR. This test case seems to be unrelated to the upper boundary of density in predprob() being 1 and not 1 + Machine$double.eps. Still working on it...

audreyyeoCH · 2024-10-10T02:04:53Z

I found some test cases failing and am working on it before I feel confident to request PR. This test case seems to be unrelated to the upper boundary of density in predprob() being 1 and not 1 + Machine$double.eps. Still working on it...

I solved it! The test case passed whenpredprob() used to check these results.

audreyyeoCH · 2024-10-16T12:38:59Z

Hm I see. I think only some names change in the output of boundsPredprob right? In that case could just have a temporary object assigned the result of it, and then rename and pass to plotBounds. I would recommend keeping that example such that later it will be easy to compare when you refactor plotBounds. So a little bit extra code now is worth it.

ahh true that - thanks! I added it back now... and plotBounds(boundsPOSTprob)) 😆 , thanks for your review!

danielinteractive

Thanks @audreyyeoCH , nice work, please see comments below

R/boundsPredprob.R

examples/boundsPredprob.R

examples/ocPredprobDist.R

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

danielinteractive · 2025-01-09T03:37:12Z

R/boundsPredprob.R

@@ -1,74 +1,86 @@
-#' Decision cutpoints for boundary (based on predictive probability)
+#' Decision cutpoints for boundary (based on predictive probability) for Decision 1 rule.


Has this been added already?

examples/boundsPredprob.R

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

audreyyeoCH · 2025-01-13T14:08:34Z

ok so I had some debugging to do...

the t(parE) seems to be duplicating the efforts of helper functions postprob() and predprob() so I removed it. Which created downward problem with ìfmissing(weight)`, so I fixed that too.

the tests are a little more improved too. The first test tests if weights are there, the second builds on what if the weights are there and there are mixed priors.

lastly, due to these changes, I wanted to

make it easy for the user to specify alpha and beta parameters in beta mixture priors
not get the answer wrong

therefore, I improved the documentation of inherited parameters of parE in postprob() and predprob() .... which I learned, don't inherit parameters from each other ... but boundsPredprob should be fine and ready for review soon.

…tation consistencies

danielinteractive

Thanks @audreyyeoCH , almost there!
Btw it would be good to soon come back to a state where only 1 PR is in the works, and the PR is as small as possible. That way, it will be quicker to finish and get to a state where all tests pass etc. again.

R/boundsPredprob.R

R/postprob.R

audreyyeoCH · 2025-01-14T09:21:54Z

Thanks @audreyyeoCH , almost there! Btw it would be good to soon come back to a state where only 1 PR is in the works, and the PR is as small as possible. That way, it will be quicker to finish and get to a state where all tests pass etc. again.

Yes for sure! I can focus on this one first since it's the oldest

danielinteractive · 2025-01-14T13:47:33Z

R/boundsPredprob.R

@@ -52,7 +52,7 @@ boundsPredprob <- function(looks, Nmax = max(looks), p0, tT, phiL, phiU, parE =
  if (missing(weights)) {
    weights <- rep(1, nrow(t(parE)))
  }
-  assert_numeric(weights, min.len = 0, len = nrow(par), finite = TRUE)
+  assert_numeric(weights, min.len = 0, len = nrow(parE), finite = TRUE)


If parE is passed as a vector then this would fail, I guess we also need t(parE), as in line 53?

audreyyeoCH and others added 3 commits May 17, 2024 23:25

Merge remote-tracking branch 'origin/HEAD'

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examples and test

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audreyyeoCH and others added 6 commits June 11, 2024 16:05

clean

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Merge branch 'main' into 96_boundsPredprob

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it works

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Merge branch 'main' into 96_boundsPredprob

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danielinteractive mentioned this pull request Sep 26, 2024

92_boundsPostprob #104

Merged

audreyyeoCH and others added 13 commits September 26, 2024 08:19

some syntax changes

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Merge branch 'main' into 96_boundsPredprob

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audreyyeoCH marked this pull request as draft October 7, 2024 21:37

added plotBounds(boundsPredprob()) examples and plotBounds(

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audreyyeoCH requested a review from danielinteractive October 17, 2024 10:44

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audreyyeoCH and others added 13 commits October 19, 2024 11:03

Update R/boundsPredprob.R

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Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

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audreyyeoCH requested a review from danielinteractive December 31, 2024 20:25

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audreyyeoCH and others added 2 commits January 9, 2025 10:49

Update examples/boundsPredprob.R

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Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

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debugging on parE issue with giving correct results and other documen…

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…tation consistencies

audreyyeoCH requested a review from danielinteractive January 13, 2025 14:14

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96 bounds predprob #105

96 bounds predprob #105

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		@@ -1,74 +1,86 @@
		#' Decision cutpoints for boundary (based on predictive probability)
		#' Decision cutpoints for boundary (based on predictive probability) for Decision 1 rule.

96 bounds predprob #105

Are you sure you want to change the base?

96 bounds predprob #105

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