Add AET01_AESI

[edelarua]

Closes insightsengineering/chevron-tasks#36

[github-actions]

🧪 $Test coverage: 89.35%$

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ---------------------------------
R/aet01_aesi.R                 188       8  95.74%   39, 41-45, 272, 285
R/aet01.R                      330       6  98.18%   38, 240, 253, 316, 322, 554
R/aet02.R                      222       2  99.10%   136, 489
R/aet03.R                       85       0  100.00%
R/aet04.R                      104       6  94.23%   81-86
R/assertions.R                  36       0  100.00%
R/checks.R                      14       0  100.00%
R/chevron_tlg-S4class.R         21       0  100.00%
R/chevron_tlg-S4methods.R       42      16  61.90%   47-55, 90-98, 218-290
R/cmt01a.R                     191       0  100.00%
R/cmt02_pt.R                    52       0  100.00%
R/dmt01.R                       40       0  100.00%
R/dst01.R                      287       0  100.00%
R/dtht01.R                     104       0  100.00%
R/egt01.R                       46       0  100.00%
R/egt02.R                       60       0  100.00%
R/egt03.R                      129      85  34.11%   32-52, 111, 125-232, 291, 305-339
R/ext01.R                       81       8  90.12%   238-241, 245-248
R/gen_args.R                     1       1  0.00%    27
R/lbt01.R                       84       0  100.00%
R/lbt04.R                       52       1  98.08%   127
R/lbt05.R                       70       2  97.14%   121, 149
R/mht01.R                       72       2  97.22%   33-34
R/mng01.R                       93       9  90.32%   113, 117-120, 133-134, 139, 182
R/pdt01.R                       61      38  37.70%   35-52, 108-150
R/utils.R                      164     109  33.54%   70, 83-212
R/vst01.R                       48       0  100.00%
R/vst02.R                      102       3  97.06%   42, 120, 257
TOTAL                         2779     296  89.35%

Results for commit: f85a2e235eca9a30ac712cd1f60983f0df2f4379

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    21 suites   1m 8s ⏱️
  99 tests   68 ✔️ 31 💤 0 ❌
218 runs  141 ✔️ 77 💤 0 ❌

Results for commit 4350488.

♻️ This comment has been updated with latest results.

[khatril]

@clarkliming @barnett11 A general comment - The optional lines (specified in aesi_vars) are displayed as default, which isn't the standard display for this output. Should we remove these optional lines and give the user option to add them in as needed? Rather than displaying them all as default?

[clarkliming]

if by default we don't have these optional lines, then we should make it the default one, instead of having other lines. However, I still thinks that the structures of "total number of xxx" and "No. of " is difficult to handle here. Since we are using labels (with spaces), I think we should, include all the summary vars in the argument, including ALL_RESOLVED and NOT_RESOLVED, SER and REL. What do you think @edelarua and @barnett11

[edelarua]

if by default we don't have these optional lines, then we should make it the default one, instead of having other lines. However, I still thinks that the structures of "total number of xxx" and "No. of " is difficult to handle here. Since we are using labels (with spaces), I think we should, include all the summary vars in the argument, including ALL_RESOLVED and NOT_RESOLVED, SER and REL. What do you think @edelarua and @barnett11

@clarkliming I think it makes sense logically to include ALL_RESOLVED/NOT_RESOLVED/SER/REL as optional vars in the argument, but an issue arises if the user chooses to include indented sub-variables without also including the related "total" var, as this would make the resulting structure of the output table quite confusing for the user.

E.g.

                                                                                      A: Drug X    B: Placebo    C: Combination
                                                                                       (N=134)       (N=134)        (N=132)    
  —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  Total number of patients with at least one AE                                      122 (91.0%)   123 (91.8%)    120 (90.9%)  
  Total number of AEs                                                                    609           622            703      
  Total number of patients with at least one AE by worst grade                                                                 
    Grade 1                                                                           7 (5.2%)      9 (6.7%)        4 (3.0%)   
    Grade 2                                                                           6 (4.5%)      10 (7.5%)       7 (5.3%)   
    Grade 3                                                                          18 (13.4%)    14 (10.4%)      16 (12.1%)  
    Grade 4                                                                          15 (11.2%)    20 (14.9%)      18 (13.6%)  
    Grade 5 (fatal outcome)                                                          76 (56.7%)    70 (52.2%)      75 (56.8%)  
  Total number of patients with study drug withdrawn due to AE                       27 (20.1%)    26 (19.4%)      30 (22.7%)  
  Total number of patients with dose modified/interrupted due to AE                  66 (49.3%)    76 (56.7%)      74 (56.1%)  
  Total number of patients with treatment received for AE                            98 (73.1%)    102 (76.1%)    103 (78.0%)  
  Total number of patients with all non-fatal AEs resolved                           84 (62.7%)    92 (68.7%)      97 (73.5%)  
    No. of patients with study drug withdrawn due to resolved AE                      9 (6.7%)      12 (9.0%)      15 (11.4%)  
    No. of patients with dose modified/interrupted due to unresolved or ongoing AE   48 (35.8%)    56 (41.8%)      59 (44.7%)  
    No. of patients with study drug withdrawn due to serious AE                       9 (6.7%)      6 (4.5%)       11 (8.3%)   
    No. of patients with treatment received for serious AE                           70 (52.2%)    73 (54.5%)      62 (47.0%)  
    No. of patients with dose modified/interrupted due to related AE                 29 (21.6%)    38 (28.4%)      38 (28.8%)  
    No. of patients with treatment received for related AE                           69 (51.5%)    74 (55.2%)      72 (54.5%)  
    No. of patients with serious, related AE                                         76 (56.7%)    70 (52.2%)      75 (56.8%)  

[barnett11]

Hi @clarkliming , @edelarua ,
The default table should be without the optional lines. We may decide if the optional lines are part of aet01_aesi_1 or aet01_aesi_2 depending on impact of programming. CENSORED presents the default as below,

[clarkliming]

looks good to me; the preprocessing and in main the aesi_vars part are complicated but we can refine later;