Template Review #140

[bozhang0112]

Close insightsengineering/chevron-tasks#45

1. AET03 Variable used changed to ASEV, AET04 variable used changed to 'ATOXGR'.
2. Removed missing ASEV/ATOXGR as part of pre-processing respectively.
3. Added another template as AET04_2 to collapse grade level 3-5.
4. Changed the structure of template of AET04 to match standards.

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/aet01.R                            312     312  0.00%    39-584
R/aet02.R                            197     197  0.00%    29-479
R/aet03.R                             69      69  0.00%    37-156
R/aet04.R                            172     172  0.00%    48-365
R/assertions.R                        42      42  0.00%    21-104
R/checks.R                            14      14  0.00%    15-48
R/chevron_tlg-S4class.R               19      19  0.00%    37-90
R/chevron_tlg-S4methods.R             14      14  0.00%    15-117
R/cmt01a.R                           156     156  0.00%    46-433
R/cmt02_pt.R                          37      37  0.00%    34-108
R/dmt01.R                             29      29  0.00%    44-125
R/dst01.R                            231     231  0.00%    5-619
R/dtht01.R                            77      77  0.00%    42-190
R/egt01.R                             44      44  0.00%    44-134
R/egt02.R                             56      56  0.00%    38-222
R/ext01.R                             69      69  0.00%    38-254
R/gen_args.R                           1       1  0.00%    19
R/lbt01.R                             39      39  0.00%    41-123
R/mht01.R                             57      57  0.00%    38-138
R/sample_study_object.R               14      14  0.00%    14-35
R/standard_data_preprocessing.R      240     240  0.00%    52-531
R/utils.R                            125     125  0.00%    11-274
R/vst01.R                             45      45  0.00%    44-136
R/vst02.R                             92      92  0.00%    39-259
TOTAL                               2151    2151  0.00%

Results for commit: 6fb7900427b1215fd0650eabd3927144ec273dac

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[barnett11]

Hi @bozhang0112
I am getting very different results to what I am expecting. In the test data, for PULMONARY EMBOLISM on Placebo I have 2 SEVERE records, but in this function it returns 0. I also seem to get different results when I restrict the data to eg. AEBODSYS="RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS" I get 1 SEVERE for PULMONARY EMBOLISM, when I restrict to AEDECOD=="PULMONARY EMBOLISM" then I get 0?

Test data location - root/clinical_studies/ro_testing/cdp_testing/spa_testing/data_analysis/spaenv_testing/qa/outdata_vad @duanx9

[wangh107]

merge after this PR:#231

[clarkliming]

it seems that this work has been paused for quite a while. Maybe @duanx9 you can pick it up?

[clarkliming]

closed because we have #324