add pdt02

[6iris6]

close insightsengineering/chevron-tasks#55

[github-actions]

Unit Tests Summary

    1 files    23 suites   1m 7s ⏱️
104 tests   72 ✔️ 32 💤 0 ❌
228 runs  147 ✔️ 81 💤 0 ❌

Results for commit 4f50873.

♻️ This comment has been updated with latest results.

[barnett11]

Thanks @6iris6 , some suggestions below,

• DVREAS is showing a rogue (n) in it's description?
• Column headers should read Primary Reason and Description
  Thanks

[6iris6]

Thanks @6iris6 , some suggestions below,

• DVREAS is showing a rogue (n) in it's description?
• Column headers should read Primary Reason and Description
  Thanks

Thanks @barnett11
1.The (n) may be from the last column, it's related to your console window length;
2. headers are updated.

[github-actions]

🧪 $Test coverage: 89.53%$

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                       95       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      12  87.10%   113, 117-120, 129-137, 182
R/pdt01.R                       61      38  37.70%   35-52, 108-150
R/pdt02.R                       68       0  100.00%
R/utils.R                      163     109  33.13%   70, 83-212
R/vst01.R                       48       0  100.00%
R/vst02.R                      102       3  97.06%   42, 120, 257
TOTAL                         2857     299  89.53%

Results for commit: e89f23ea9d7bb319e42d8faac330f622976e6675

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[barnett11]

Thanks @6iris6 , some suggestions below,

• DVREAS is showing a rogue (n) in it's description?
• Column headers should read Primary Reason and Description
  Thanks

Thanks @barnett11 1.The (n) may be from the last column, it's related to your console window length; 2. headers are updated.

I've looked and I'm pretty sure it's not wrapping, appears in every variation of text that i create for DVREAS?

[6iris6]

Thanks @6iris6 , some suggestions below,

• DVREAS is showing a rogue (n) in it's description?
• Column headers should read Primary Reason and Description
  Thanks

Thanks @barnett11 1.The (n) may be from the last column, it's related to your console window length; 2. headers are updated.

I've looked and I'm pretty sure it's not wrapping, appears in every variation of text that i create for DVREAS?

Apologize, my misunderstanding. Do you want to remove (n) @barnett11 ? I got it from the TLG-C PDT02
https://docs.roche.com/#/tlg-catalog/devel/tables/safety/pdt02.html

[barnett11]

Thanks @6iris6 , some suggestions below,

• DVREAS is showing a rogue (n) in it's description?
• Column headers should read Primary Reason and Description
  Thanks

Thanks @barnett11 1.The (n) may be from the last column, it's related to your console window length; 2. headers are updated.

I've looked and I'm pretty sure it's not wrapping, appears in every variation of text that i create for DVREAS?

Apologize, my misunderstanding. Do you want to remove (n) @barnett11 ? I got it from the TLG-C PDT02 https://docs.roche.com/#/tlg-catalog/devel/tables/safety/pdt02.html

The (n) is not in the template so I'd advise to remove thanks @6iris6

[edelarua]

Hi @barnett11, Iris is out of office so I will be finishing up this PR for her. I have removed the (n) from the table labels so this should be ready for another review now. Thanks!

[barnett11]

Hi @edelarua
Thanks for this, unfortunately the layout still isn't quite right, and numbers not matching expected - the display should be as below, with DVREAS being shown as nn(xx.x%). I've added mockup to original request, and adding below also for reference,

[edelarua]

Hi @edelarua Thanks for this, unfortunately the layout still isn't quite right, and numbers not matching expected - the display should be as below, with DVREAS being shown as nn(xx.x%).

Hi @barnett11, I have updated the value formats to match the mockup. Regarding the numbers not matching expected - could you send me sample expected output for syn_data (or other sample data) so I can compare values against it?

[barnett11]

Hi @edelarua ,
I beleive DVREAS is counting all occurrences, and not patients - please see my test example below showing this,

[edelarua]

@barnett11 I have opened a PR in tern (insightsengineering/tern#799) to fix the label/value formatting in summarize_num_patients. Once that is merged this should be properly formatted (labels & value formats). I will let you know once that is done.

Also, should the DVTERM counts be counting occurrences or patients?

EDIT: @barnett11 This is now done and the template should be outputting correctly. Let me know if any other changes are needed!

Changes have been implemented

[edelarua]

@barnett11 this is ready for another review