698 improve test coverage in design methodsr

[Puzzled-Face]

This PR increases test coverage from 15% to 72%.

Generally speaking, code dealing with placebo and sentinel patients is not currently covered.

• simulate-DualDesign appears to produce inconsistent results
• simulate-DADesign appears to produce inconsistent results
• simulate-DualResponsesSamplesDesign is almost 1000 lines long

Next steps are to move design generation code into helper functions and generalise to allow for the inclusion of placebo patients.

[github-actions]

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                147       5  96.60%   43, 564-565, 571-576
R/Data-methods.R              203       0  100.00%
R/Data-validity.R             144       1  99.31%   21
R/Design-class.R              321       0  100.00%
R/Design-methods.R           2788     779  72.06%   154-158, 174-181, 659-663, 687-690, 698-717, 722-751, 755-756, 758, 773-781, 785, 797-816, 1215-1219, 1346, 1360-1364, 1426, 1616, 1833, 1860-1863, 1872-1883, 1887-1906, 1917-1921, 1927-1939, 2194, 2219-2222, 2229-2240, 2244-2263, 2275-2279, 2285-2297, 2571-2574, 2602-2605, 2613-2625, 2628-2639, 2643-2679, 2696-2705, 2711-2726, 2751, 2792-2793, 3046-3508, 3603-3614, 3617-3628, 3632-3668, 3685-3694, 3702-3717, 3755, 3797-3798, 4069, 4071-4072, 4131, 4167, 4204-4207, 4226-4230, 4291-4298, 4326-4330, 4338-4356, 4382-4401, 4404, 4437, 4459-4477, 4711, 4805
R/Design-validity.R            28       0  100.00%
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               84       1  98.81%   139
R/helpers_design.R             75      35  53.33%   77-129
R/helpers_jags.R               77       0  100.00%
R/helpers_model.R              78       4  94.87%   38, 89-90, 139
R/helpers_rules.R             428       0  100.00%
R/helpers_simulations.R        18       0  100.00%
R/helpers.R                   224      61  72.77%   107-127, 162-178, 200-304, 339-353
R/logger.R                     11       0  100.00%
R/mcmc.R                      287      18  93.73%   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, 3367-3369, 3371-3372, 3375-3380
R/Model-methods.R             418      32  92.34%   78, 710-755, 1076-1085
R/Model-validity.R            435       8  98.16%   430-433, 442-445
R/ModelParams-class.R          17       0  100.00%
R/ModelParams-validity.R       21       0  100.00%
R/Rules-class.R               431       2  99.54%   3150, 3231
R/Rules-methods.R            1482     166  88.80%   889, 892, 895, 1010, 1013, 1016, 1136-1139, 1173, 1276-1279, 1314, 2477-2485, 2509-2516, 3019-3262, 3531, 3535, 3580, 3584
R/Rules-validity.R            418       0  100.00%
R/Samples-class.R               6       0  100.00%
R/Samples-methods.R          1188      47  96.04%   405-415, 643, 1413-1448, 1660-1661, 1693, 1706, 1888, 2218-2223
R/Samples-validity.R           10       0  100.00%
R/Simulations-class.R         199       5  97.49%   770-773, 1028
R/Simulations-methods.R      1604    1460  8.98%    65-350, 406, 416-435, 448-453, 500-509, 675-2944
R/Simulations-validity.R       75      75  0.00%    20-168
R/utils.R                       6       0  100.00%
TOTAL                       12712    2944  76.84%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  -------
R/Design-methods.R           0   -1096  +39.31%
R/Model-methods.R            0      -2  +0.48%
R/Rules-methods.R            0      -2  +0.13%
R/Samples-methods.R        +35      +2  -0.05%
R/Simulations-class.R        0     -24  +12.06%
TOTAL                      +35   -1122  +8.91%

Results for commit: 54a3b1f

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

       1 files       38 suites   3m 10s ⏱️
1 214 tests 1 061 ✔️ 153 💤 0 ❌
6 502 runs  6 311 ✔️ 191 💤 0 ❌

Results for commit 54a3b1f.

♻️ This comment has been updated with latest results.

[danielinteractive]

thanks @Puzzled-Face for the initiative, much appreciated - please see comments below

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
CrmPackClass-class	💔	$22.07$	$+10.24$	$0$	$0$	$0$	$0$
CrmPackClass-methods	💚	$22.38$	$-2.67$	$0$	$0$	$0$	$0$
Design-methods	💔	$21.62$	$+10.12$	$+11$	$+11$	$0$	$0$
Rules-methods	💚	$50.79$	$-4.03$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
CrmPackClass-class	💔	$21.92$	$+10.24$	CrmPackClass_correctly_identifies_crmPack_classes
CrmPackClass-methods	💚	$22.38$	$-2.67$	tidy_methods_exist_for_all_relevant_classes
Design-methods	👶		$+3.24$	examine_produces_consistent_results
Design-methods	👶		$+2.32$	examine_produces_consistent_results_with_placebo_data
Design-methods	👶		$+0.72$	simulate_DualDesign_produces_consistent_results
Design-methods	👶		$+2.01$	simulate_DualResponsesDesign_produces_consistent_results
Design-methods	👶		$+0.30$	simulate_DualResponsesSamplesDesign_produces_consistent_results
Design-methods	👶		$+0.20$	simulate_RuleDesign_produces_consistent_results
Design-methods	👶		$+0.47$	simulate_TDDesign_produces_consistent_results
Design-methods	👶		$+0.33$	simulate_TDSamplesDesign_produces_consistent_results
Design-methods	👶		$+0.62$	simulate_produces_consistent_results_with_placebo_data
Design-methods	👶		$+0.83$	simulate_produces_consistent_results_with_sentinel_patients
Rules-methods	💚	$15.18$	$-1.46$	stopTrial_works_correctly_for_StoppingTDCIRatio_when_samples_are_not_provided

Results for commit ddf0b83

♻️ This comment has been updated with latest results.