temporary suggestion for testing simulate for design class #802

robertadamsbayer · 2024-03-20T08:10:21Z

Pull Request

Fixes #798

robertadamsbayer · 2024-03-20T08:13:57Z

Hello @danielinteractive please review the suggestion for testing. I tried both, the scenario with fixed seeds (checking the full mySims object, thus inherently checking all subsequent scenarios) and the scenario which just checks for the "meta data" (i.e. lengths, classes etc.). Before continuing to apply that to all other methods in Design-methods I wanted to check in and ask for best-practice guidance. Also, I would suggest, if we agree on the testing strategy, to do all Design-methods testing in one branch / PR then because it will be quite straight forward to implement and review?

github-actions · 2024-03-20T08:21:17Z

Code Coverage Summary

Filename                         Stmts    Miss  Cover    Missing
-----------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                       73       1  98.63%   72
R/crmPack-package.R                  4       0  100.00%
R/CrmPackClass-methods.R             5       0  100.00%
R/Data-class.R                     156       5  96.79%   43, 565-566, 572-577
R/Data-methods.R                   267       0  100.00%
R/Data-validity.R                  144       1  99.31%   21
R/Design-class.R                   391       0  100.00%
R/Design-methods.R                2775     771  72.22%   563-567, 591-594, 602-621, 626-655, 659-660, 662, 677-685, 689, 701-720, 1122-1126, 1253, 1267-1271, 1333, 1523, 1740, 1767-1770, 1779-1790, 1794-1813, 1824-1828, 1834-1846, 2109, 2134-2137, 2144-2155, 2159-2178, 2190-2194, 2200-2212, 2496-2499, 2527-2530, 2538-2550, 2553-2564, 2568-2604, 2621-2630, 2636-2651, 2676, 2717-2718, 2981-3451, 3546-3557, 3560-3571, 3575-3611, 3628-3637, 3645-3660, 3698, 3740-3741, 4020, 4022-4023, 4082, 4118, 4155-4158, 4177-4181, 4242-4249, 4277-4281, 4289-4307, 4333-4352, 4355, 4388, 4410-4428, 4697, 4792
R/Design-validity.R                 38      10  73.68%   47-56
R/fromQuantiles.R                  176      67  61.93%   238-378
R/helpers_broom.R                   74      10  86.49%   30, 34-35, 37-38, 40, 81, 102-104
R/helpers_covr.R                    23       0  100.00%
R/helpers_data.R                    96       1  98.96%   139
R/helpers_design.R                 126      36  71.43%   22, 77-129
R/helpers_jags.R                    77       0  100.00%
R/helpers_kintr_Increments.R       156       2  98.72%   191, 278
R/helpers_knitr_CohortSize.R       100       0  100.00%
R/helpers_knitr_GeneralData.R      183      61  66.67%   18, 67-70, 83-86, 99-102, 114-117, 130-133, 155-157, 240-244, 253-298, 346, 351
R/helpers_model.R                   85       4  95.29%   38, 89-90, 139
R/helpers_rules.R                  428       0  100.00%
R/helpers_samples.R                  5       0  100.00%
R/helpers_simulations.R             27       0  100.00%
R/helpers.R                        214      61  71.50%   107-127, 162-178, 200-304, 339-353
R/logger.R                          11       0  100.00%
R/mcmc.R                           290      18  93.79%   92-97, 376-377, 387, 389-390, 393-396, 579-580, 669, 675, 733
R/McmcOptions-class.R               22       0  100.00%
R/McmcOptions-methods.R              8       1  87.50%   43
R/McmcOptions-validity.R            42       0  100.00%
R/Model-class.R                   1062     166  84.37%   145-147, 216-218, 222-224, 283-285, 357-359, 363-365, 444-446, 513-515, 577-581, 584-587, 690-693, 697-698, 813-817, 937-939, 943-951, 1096-1098, 1103-1106, 1110-1113, 1229-1233, 1235-1238, 1242-1245, 1248, 1409-1419, 1424-1430, 1585-1588, 1594-1601, 1758, 1767, 1776, 1785, 1794-1799, 1935, 1944, 1953, 1961-1963, 2807-2836, 2840-2846, 2853-2857, 2862, 2969-2982, 3008, 3104-3106, 3110, 3203-3205, 3209, 3278-3290, 3308, 3368-3370, 3372-3373, 3376-3381
R/Model-methods.R                  472      38  91.95%   78, 233-238, 809-854, 1175-1184
R/Model-validity.R                 443      16  96.39%   430-433, 442-445, 596-604
R/ModelParams-class.R               17       0  100.00%
R/ModelParams-validity.R            21       0  100.00%
R/Rules-class.R                    458       0  100.00%
R/Rules-methods.R                 1541     184  88.06%   889, 892, 895, 1010, 1013, 1016, 1136-1139, 1173, 1276-1279, 1314, 2582-2590, 2614-2621, 2784-2793, 3073-3082, 3215-3458, 3745, 3749, 3794, 3798
R/Rules-validity.R                 448      30  93.30%   684-723
R/Samples-class.R                    6       0  100.00%
R/Samples-methods.R               1188      21  98.23%   410-420, 648, 1665-1666, 1698, 1711, 1893, 2223-2228
R/Samples-validity.R                10       0  100.00%
R/Simulations-class.R              208       5  97.60%   769-772, 1028
R/Simulations-methods.R           1617    1473  8.91%    65-350, 406, 416-435, 448-453, 500-509, 674-2969
R/Simulations-validity.R            75      75  0.00%    20-168
R/utils.R                            6       0  100.00%
TOTAL                            13568    3057  77.47%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/checkmate.R           -14      -1  +0.93%
R/fromQuantiles.R        +4     +15  -7.84%
R/helpers_design.R        0      -6  +4.76%
TOTAL                   -10      +8  -0.90%

Results for commit: f19a571

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

danielinteractive

thanks @robertadamsbayer for the nice work! please see feedback below - I would simplify this further. yes, once agreed, we can put many tests in the same PR. no need to shoot for everything right away though, because then the PR gets again too large and takes too much time. incremental progress here is still best too

danielinteractive · 2024-03-20T08:30:15Z

tests/testthat/test-helpers_design.R

+    rng_kind = "Mersenne-Twister",
+    rng_seed = 1234
+  )
+  time <- system.time(mySims <- simulate(design,


do we need to time this simulation run? (not sure, because time is also not used below and would anyway differ between platforms)

fully agree - was a bit lazy from me taking that over from the examples...

danielinteractive · 2024-03-20T08:31:39Z

tests/testthat/test-helpers_design.R

+  expect_class(mySims, "Simulations")
+
+  expect_equal(any(sapply(mySims@fit[[1]], is.numeric)), TRUE) # check if all elements in mySims@fit are numeric
+
+  expect_equal(length(mySims@stop_report), 5) # check for length
+
+  expect_logical(mySims@stop_report) # check for stop_report to be logical vector


something like this would be sufficient

danielinteractive · 2024-03-20T08:31:58Z

tests/testthat/test-helpers_design.R

+    ),
+  ))[3]
+
+  expected <-


this is too detailed / too much maintenance when numbers change etc.

Thanks for guidance! I will adopt.

@danielinteractive Hi Daniel, I put the new "end-to-end" test for simulate in "test-helpers_design.R". When moving it over to "test-Design-methods.R" I realized that there are already tests (using snapshots) for simulate (and different classes) already implemented. Those use fixed rng seeds, therefore "mimicking" quite closely what you suggested not to do. I don´t know what to keep and what to get rid of there?!

I would just leave existing tests. More coverage does not hurt us

github-actions · 2024-03-20T08:52:57Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
CrmPackClass-methods	💚	$59.73$	$-10.26$	$0$	$0$	$0$	$0$
Design-methods	💔	$46.33$	$+4.66$	$+46$	$0$	$0$	$+1$
Rules-methods	💔	$49.37$	$+4.30$	$0$	$0$	$0$	$0$
Samples-methods	💔	$30.21$	$+1.02$	$0$	$0$	$0$	$0$
fromQuantiles	💀	$0.03$	$-0.03$	$-8$	$0$	$0$	$0$
helpers_knitr	💔	$27.84$	$+3.53$	$+11$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
CrmPackClass-methods	💚	$30.08$	$-5.68$	tidy_methods_exist_for_all_relevant_classes
CrmPackClass-methods	💚	$29.65$	$-4.58$	tidy_methods_return_non_empty_value_for_all_classes
Design-methods	👶		$+0.94$	simulate_DualDesign_produces_consistent_results_with_sentinel_patients
Design-methods	👶		$+1.53$	simulate_for_the_class_design_returns_correct_objects
Design-methods	👶		$+0.92$	simulate_for_the_class_design_with_placebo_and_sentinel_patients_returns_correct_objects
Design-methods	👶		$+1.12$	simulate_for_the_class_design_with_placebo_returns_correct_objects
Rules-methods	💔	$13.45$	$+2.09$	stopTrial_works_correctly_for_StoppingTDCIRatio_when_samples_are_not_provided
Rules-methods	💔	$10.89$	$+1.53$	stopTrial_works_correctly_for_StoppingTDCIRatio_when_samples_are_provided
Samples-methods	💔	$0.25$	$+1.42$	size_Samples_returns_correct_number_of_samples
Simulations-class	💀	$0.01$	$-0.01$	.DefaultPseudoSimulations_cannot_be_instantiated_directly
Simulations-class	💀	$0.01$	$-0.01$	PseudoSimulations_generator_function_works_as_expected
Simulations-class	💀	$0.03$	$-0.03$	PseudoSimulations_object_can_be_created_with_the_user_constructor
Simulations-class	💀	$0.00$	$-0.00$	PseudoSimulations_user_constructor_argument_names_are_as_expected
fromQuantiles	💀	$0.03$	$-0.03$	h_get_min_inf_beta_works_as_expected_with_p_q
helpers_knitr	💔	$27.03$	$+3.03$	asis_parameter_works_correctly_for_all_implemented_methods

Results for commit abf2c65

♻️ This comment has been updated with latest results.

…ithub.com/Roche/crmPack into 798_code_coverage_for_simulate_for_design

Merge branch '798_code_coverage_for_simulate_for_design' of https://github.com/Roche/crmPack into 798_code_coverage_for_simulate_for_design # Conflicts: # tests/testthat/test-Design-methods.R

…602-621 in Deisn-methods, partially - not yet for placebo)

robertadamsbayer · 2024-03-27T19:06:25Z

Hi @danielinteractive - in DualDesign there are placebo clauses which are not covered in tests yet (indicated by the missing rows in test coverage). When I create a dual design which contains placebo data and try to pass that to simulate I get the following error:

Do we have a working example for DualDesign with placebo or ist that somehow a special case that I am not aware of?

danielinteractive · 2024-03-28T08:08:23Z

Thanks @robertadamsbayer , I would check the examples folder, if there is nothing it might be a bug ... and we would need to fix it

danielinteractive · 2024-05-03T07:55:17Z

This PR is parked for now, in order to prioritize tests for Simulation methods.

temporary suggestion for testing simulate for design class

14cf5e0

robertadamsbayer requested a review from danielinteractive as a code owner March 20, 2024 08:10

robertadamsbayer linked an issue Mar 20, 2024 that may be closed by this pull request

Code coverage for design methods #797

Open

11 tasks

[skip style] [skip vbump] Restyle files

e7bdd69

danielinteractive reviewed Mar 20, 2024

View reviewed changes

robertadamsbayer and others added 8 commits March 27, 2024 17:45

Extended structural tests for simulate for Design

f239a50

Merge branch '798_code_coverage_for_simulate_for_design' of https://g…

ae859cf

…ithub.com/Roche/crmPack into 798_code_coverage_for_simulate_for_design

extended testing for simulate for Design

f19a571

[skip style] [skip vbump] Restyle files

689c80a

Added more tests for simulate for Design

bb38882

commit to merge

a485f2c

Merge branch '798_code_coverage_for_simulate_for_design' of https://github.com/Roche/crmPack into 798_code_coverage_for_simulate_for_design # Conflicts: # tests/testthat/test-Design-methods.R

DualDesign tests for sentinel patients (covers missing tests for row …

9515115

…602-621 in Deisn-methods, partially - not yet for placebo)

[skip style] [skip vbump] Restyle files

ce6105a

danielinteractive marked this pull request as draft June 13, 2024 14:33

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

temporary suggestion for testing simulate for design class #802

temporary suggestion for testing simulate for design class #802

robertadamsbayer commented Mar 20, 2024 •

edited

Loading

robertadamsbayer commented Mar 20, 2024

github-actions bot commented Mar 20, 2024 •

edited

Loading

danielinteractive left a comment

danielinteractive Mar 20, 2024

robertadamsbayer Mar 20, 2024

danielinteractive Mar 20, 2024

danielinteractive Mar 20, 2024

robertadamsbayer Mar 20, 2024

robertadamsbayer Mar 20, 2024 •

edited

Loading

danielinteractive Mar 20, 2024

github-actions bot commented Mar 20, 2024 •

edited

Loading

robertadamsbayer commented Mar 27, 2024 •

edited

Loading

danielinteractive commented Mar 28, 2024

danielinteractive commented May 3, 2024

temporary suggestion for testing simulate for design class #802

Are you sure you want to change the base?

temporary suggestion for testing simulate for design class #802

Conversation

robertadamsbayer commented Mar 20, 2024 • edited Loading

Pull Request

robertadamsbayer commented Mar 20, 2024

github-actions bot commented Mar 20, 2024 • edited Loading

Code Coverage Summary

Diff against main

danielinteractive left a comment

Choose a reason for hiding this comment

danielinteractive Mar 20, 2024

Choose a reason for hiding this comment

robertadamsbayer Mar 20, 2024

Choose a reason for hiding this comment

danielinteractive Mar 20, 2024

Choose a reason for hiding this comment

danielinteractive Mar 20, 2024

Choose a reason for hiding this comment

robertadamsbayer Mar 20, 2024

Choose a reason for hiding this comment

robertadamsbayer Mar 20, 2024 • edited Loading

Choose a reason for hiding this comment

danielinteractive Mar 20, 2024

Choose a reason for hiding this comment

github-actions bot commented Mar 20, 2024 • edited Loading

Unit Test Performance Difference

robertadamsbayer commented Mar 27, 2024 • edited Loading

danielinteractive commented Mar 28, 2024

danielinteractive commented May 3, 2024

robertadamsbayer commented Mar 20, 2024 •

edited

Loading

github-actions bot commented Mar 20, 2024 •

edited

Loading

robertadamsbayer Mar 20, 2024 •

edited

Loading

github-actions bot commented Mar 20, 2024 •

edited

Loading

robertadamsbayer commented Mar 27, 2024 •

edited

Loading