Refactor setSeed and getResultList #676

0liver0815 · 2023-09-14T13:25:29Z

Closes a part of #671

danielinteractive

Thanks a lot @0liver0815 , much appreciated, please see few comments below

R/Design-methods.R

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

…ithub.com/Roche/crmPack into 671-clean_design_methods_seed_resultslist

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

github-actions · 2023-09-14T16:09:32Z

Unit Tests Summary

      1 files     35 suites 2m 44s ⏱️
1 161 tests 1 033 ✔️ 128 💤 0 ❌
6 119 runs 5 956 ✔️ 163 💤 0 ❌

Results for commit a116a27.

♻️ This comment has been updated with latest results.

danielinteractive · 2023-09-14T16:14:40Z

@0liver0815 seems there are some failing unit tests:

let me know if you need help with that

github-actions · 2023-09-15T10:13:06Z

Code Coverage Summary

Filename                    Stmts    Miss  Cover    Missing
------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                  49       0  100.00%
R/crmPack-package.R             4       0  100.00%
R/Data-class.R                 80       4  95.00%   455-456, 460-465
R/Data-methods.R              202       0  100.00%
R/Data-validity.R             144       1  99.31%   21
R/Design-class.R               68       0  100.00%
R/Design-methods.R           2721    2368  12.97%   36, 95-147, 255, 280-283, 291-302, 306-325, 337-341, 347-360, 518-1083, 1148-1489, 1540, 1730, 1900-4705
R/Design-validity.R            10       0  100.00%
R/fromQuantiles.R             178      69  61.24%   237-378
R/helpers_covr.R               23       0  100.00%
R/helpers_data.R               84       1  98.81%   139
R/helpers_jags.R               77       0  100.00%
R/helpers_model.R              78       4  94.87%   38, 89-90, 139
R/helpers_rules.R             447       0  100.00%
R/helpers.R                   277     103  62.82%   103-118, 166-171, 187, 200-214, 250-447, 477-526
R/logger.R                     11       0  100.00%
R/mcmc.R                      287      18  93.73%   90-95, 374-375, 385, 387-388, 391-394, 577-578, 667, 673, 731
R/McmcOptions-class.R          18       0  100.00%
R/McmcOptions-methods.R         8       1  87.50%   43
R/McmcOptions-validity.R       42       0  100.00%
R/Model-class.R               954     155  83.75%   135-137, 205-207, 211-213, 272-274, 346-348, 352-354, 433-435, 502-504, 566-570, 573-576, 679-682, 686-687, 802-806, 926-928, 932-940, 1085-1087, 1092-1095, 1099-1102, 1218-1222, 1224-1227, 1231-1234, 1237, 1395-1405, 1410-1416, 1571-1574, 1580-1587, 1744, 1753, 1762, 1771, 1780-1785, 1921, 1930, 1939, 1947-1949, 2685-2714, 2718-2724, 2731-2735, 2740, 2845-2858, 2884, 2980-2982, 2986, 3079-3081, 3085, 3154-3166, 3184
R/Model-methods.R             376      34  90.96%   78, 155, 208, 675-720, 1039-1048
R/Model-validity.R            435       8  98.16%   430-433, 442-445
R/ModelParams-class.R          13       0  100.00%
R/ModelParams-validity.R       21       0  100.00%
R/Rules-class.R               392       2  99.49%   3068, 3130
R/Rules-methods.R            1423     161  88.69%   741, 744, 887, 890, 893, 1008, 1011, 1014, 1134-1137, 1171, 1274-1277, 1312, 2473-2481, 2505-2512, 3014-3254
R/Rules-validity.R            418       0  100.00%
R/Samples-class.R               1       0  100.00%
R/Samples-methods.R          1104      45  95.92%   406-416, 644, 1358-1393, 1616, 1629, 1794, 2124-2129
R/Samples-validity.R           10       0  100.00%
R/Simulations-class.R          49      32  34.69%   470-819
R/Simulations-methods.R      1597    1454  8.95%    65-350, 406, 416-435, 448-453, 500-509, 675-2935
R/utils.R                       6       0  100.00%
TOTAL                       11607    4460  61.57%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/Design-methods.R       +7      +7  -0.03%
TOTAL                    +7      +7  -0.04%

Results for commit: f4a299b

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

0liver0815 · 2023-09-15T11:45:45Z

@0liver0815 seems there are some failing unit tests: let me know if you need help with that

Thanks for offering. I finally found the problem. I changed RNGkind to RNGkind("Super-Duper")
https://github.com/Roche/crmPack/blob/6c6fd66085516e3ee56affeba9ce11b47cdfd175/tests/testthat/test-Design-methods.R#L14
in one of the tests, which had downstream interference with some other unit tests. I reset back to RNGkind("default") at the end of the unit test, which solved the problem.

R/Design-methods.R

* Refactor setSeed and getResultList (#676) Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * 675: Add `DesignGrouped` (#677) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes first cohort logic for grouped design simulation (#684) * Remove references to is.bool and is.scalar (#686) * Remove references to is.bool and is.scalar * [skip actions] Restyle files * Responding to review comments * Removing lintr moan * Updating documentation --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove plot.gtable and print.gtable (#697) * Remove plot.gtable and print.gtable * Fix _pkgdown.yaml * 690 remove safeinteger and iswholenumber 1 (#693) * Remove safeInteger and is.wholenumber * Fixing false test failures * [skip actions] Restyle files --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove noOverlap (#695) * remove %~% (#689) * remove %~% * Fixing NAMESPACE * 699 remove multiplot (#700) * Remove multiplot * Correct typo * Correcting typo in argument to assert_integerish * New commit for additional statistics (#663) * New commit for additional statistics * [skip actions] Restyle files * Update: additional statstics added to other designs bug correction suggetions by Clara * bug corrected * Update: Additional_stats * update: additional_stats * updaze: error_corrections (additional_stats) * update: additional_statistics * Dynamic: Additional_statistical_summary * Additional statistical summary function update * additional statistical summary changes * Update: Additional Statistical Summary * small change: additional stat summary * Suggested changes: additional_statistics and validation * [skip actions] Restyle files * Simulation refectoring * Simulation small update * [skip actions] Restyle files * small update * incorrectly named file:delete * removing documentation errors * update yaml file --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Clara <clara.beck@bayer.com> Co-authored-by: Oliver Boix <95433070+0liver0815@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> * Refactor myBarplot (#703) * Refactor myBarplot * [skip actions] Restyle files * Responding to lintr complaints * Rsponding to review comments --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --------- Co-authored-by: Oliver Boix <95433070+0liver0815@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Prerana Chandratre <82475780+Prerana17@users.noreply.github.com> Co-authored-by: Clara <clara.beck@bayer.com>

Refactor setSeed and getResultList

1c97983

0liver0815 requested a review from danielinteractive as a code owner September 14, 2023 13:25

0liver0815 and others added 2 commits September 14, 2023 13:25

Merge 1c97983 into 8bb205e

5b75de7

[skip actions] Restyle files

f900764

danielinteractive self-assigned this Sep 14, 2023

Empty-Commit

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0liver0815 and others added 7 commits September 14, 2023 16:06

Update R/Design-methods.R

365ca69

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

Update R/Design-methods.R

452d89c

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

Revise code of set_seed.

1cfdf31

Update R/Design-methods.R

2670ba7

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

Update R/Design-methods.R

e2b3b52

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

Update doc.

c0877aa

Merge branch '671-clean_design_methods_seed_resultslist' of https://g…

01cab5a

…ithub.com/Roche/crmPack into 671-clean_design_methods_seed_resultslist

0liver0815 and others added 8 commits September 14, 2023 16:45

Update R/Design-methods.R

3fdf7ea

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

Merge 3fdf7ea into 1762da7

bca48ee

[skip actions] Restyle files

6c38b0c

Convert seed silently to integer.

413833e

Update doc.

85a4f0c

Update R/Design-methods.R

ff5d6bc

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

Update doc.

c2f67a2

Correct linter finding.

661d3f0

Merge branch 'main' into 671-clean_design_methods_seed_resultslist

159efc9

0liver0815 added 2 commits September 15, 2023 11:43

Correct error.

7a13770

Change RNGkind back to default (had caused test case errors).

6c6fd66

danielinteractive approved these changes Sep 15, 2023

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Remove rng_state assignment.

a116a27

danielinteractive enabled auto-merge (squash) September 15, 2023 12:03

danielinteractive merged commit a804814 into main Sep 15, 2023
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danielinteractive deleted the 671-clean_design_methods_seed_resultslist branch September 15, 2023 13:09

Puzzled-Face mentioned this pull request Oct 16, 2023

Implement the LogisticLogNormalOrdinal class (#708) #709

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Refactor setSeed and getResultList #676

Refactor setSeed and getResultList #676

0liver0815 commented Sep 14, 2023

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0liver0815 commented Sep 15, 2023

Refactor setSeed and getResultList #676

Refactor setSeed and getResultList #676

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