675: Add `DesignGrouped` #677

danielinteractive · 2023-09-14T16:04:50Z

closes #675

github-actions · 2023-09-14T16:26:04Z

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               75       0  100.00%
R/Design-methods.R           2762    2333  15.53%   114, 139-142, 150-161, 165-184, 196-200, 206-219, 377-942, 1007-1348, 1399, 1589, 1759-4564, 4684
R/Design-validity.R            20       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_design.R             75      36  52.00%   22, 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             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            1429     164  88.52%   741, 744, 887, 890, 893, 1008, 1011, 1014, 1134-1137, 1171, 1274-1277, 1312, 2475-2483, 2507-2514, 3017-3260
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                       11746    4464  62.00%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/Design-class.R          +7       0  +100.00%
R/Design-methods.R       +41     -35  +2.56%
R/Design-validity.R      +10       0  +100.00%
R/helpers_design.R       +75     +36  +52.00%
R/Rules-methods.R         +6      +3  -0.16%
TOTAL                   +139      +4  +0.42%

Results for commit: 1fd05f6

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-09-14T17:30:52Z

Unit Tests Summary

      1 files     36 suites 2m 16s ⏱️
1 172 tests 1 044 ✔️ 128 💤 0 ❌
6 181 runs 6 018 ✔️ 163 💤 0 ❌

Results for commit ae051f4.

♻️ This comment has been updated with latest results.

R/Design-class.R

R/Design-methods.R

R/Design-validity.R

Puzzled-Face

All good. Am happy with the "we will do it later" responses.

* 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>

Daniel Sabanes Bove and others added 25 commits September 12, 2023 15:25

add class with constructors

7270a9a

add tests for model class

74ab101

add prob method

e297b77

progress

c4c2342

dose and prob function generics result now pass through add. args

697bb7b

fit and plot method tests

b871745

remove dummy tests because now we have the actual ones

f2cb21f

Merge f2cb21f into 8bb205e

fc5da18

[skip actions] Restyle files

7538012

remove indentation linter because it is not in defaults to avoid warn

d2eaa63

polishing

3a4fdf3

add DesignGrouped class

e43cbc0

also test validation fun

33071f7

start simulate method

88366e2

add example

5931e40

add tests

417c34f

Merge remote-tracking branch 'origin/main' into 675_DesignGrouped

e37fa92

forward ... from nextBest call to prob, dose, gain calls inside

ed686cf

same for stopTrial methods

4de7981

remove helper NeedsExtraProbModel as it is no longer needed

725edf9

Merge remote-tracking branch 'origin/main' into 675_DesignGrouped

ef7f82f

add back indentation_linter because it is needed with 3.1 lintr pkg

04e7f6a

add missing assertion

76a05da

add to pkgdown

ef01b23

Merge ef01b23 into 153a71a

864bd03

danielinteractive requested a review from Puzzled-Face September 14, 2023 16:09

danielinteractive assigned Puzzled-Face Sep 14, 2023

github-actions bot and others added 2 commits September 14, 2023 16:12

[skip actions] Restyle files

873bb0a

trigger checks

b5f7e34

avoid in_sim being passed to dose

3e958eb

Puzzled-Face reviewed Sep 15, 2023

View reviewed changes

Daniel Sabanes Bove and others added 6 commits September 15, 2023 15:07

address review comments

4a48ee3

Merge 4a48ee3 into 153a71a

7009236

[skip actions] Restyle files

a9b80bb

few fixes

4a4b897

Merge branch 'main' into 675_DesignGrouped

8405ef9

amend news, move helpers to separate file, adapt to main changes,tests

692761f

danielinteractive requested a review from Puzzled-Face September 15, 2023 13:44

fix line lengths

daf83d2

Puzzled-Face approved these changes Sep 15, 2023

View reviewed changes

danielinteractive enabled auto-merge (squash) September 15, 2023 13:49

Daniel Sabanes Bove added 2 commits September 15, 2023 20:37

fix typo

73b94f4

fix warning and note

ae051f4

danielinteractive merged commit 7c6ed0e into main Sep 16, 2023
19 checks passed

danielinteractive deleted the 675_DesignGrouped branch September 16, 2023 20:31

Puzzled-Face mentioned this pull request Oct 16, 2023

Implement the LogisticLogNormalOrdinal class (#708) #709

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

675: Add `DesignGrouped` #677

675: Add `DesignGrouped` #677

danielinteractive commented Sep 14, 2023

github-actions bot commented Sep 14, 2023 •

edited

Loading

github-actions bot commented Sep 14, 2023 •

edited

Loading

Puzzled-Face left a comment

675: Add DesignGrouped #677

675: Add DesignGrouped #677

Conversation

danielinteractive commented Sep 14, 2023

github-actions bot commented Sep 14, 2023 • edited Loading

Code Coverage Summary

Diff against main

github-actions bot commented Sep 14, 2023 • edited Loading

Unit Tests Summary

Puzzled-Face left a comment

Choose a reason for hiding this comment

675: Add `DesignGrouped` #677

675: Add `DesignGrouped` #677

github-actions bot commented Sep 14, 2023 •

edited

Loading

github-actions bot commented Sep 14, 2023 •

edited

Loading