Safety reports for EU submission

[yangx61]

Goal/Success Critieria

Create the following tables using tern/rtables so that EU access group can generate the summary using NEST. Moving from entimice/STREAM to NEST hopefully will significantly reduce the time needed to generate these results.

additional information

• Full table can be found here

• Some components similar to FSTG02

• We will start with safty-tte summary as the first pilot.

Ensure in tern, that the s_* with the summaries exists.

Needed Data

• ADTTE with variables AESOC, AEPT

Needed Summaries

• Patients
  • n:
  • %: n/N
• Patient with Event
  • n: ADAE$abc == 'Y'
  • %: n/N
• Censored
• Log Rank
• Hazard Ratio
  • Convergence Status:
• Interaction Test

Example

Tecentriq HCC as a fairly recent example

Example outputs for one data cut: root/clinical_studies/RO5541267/CDT30091/YO40245/data_analysis/ACE_29NOV2019/prod/output

Additional data sets (beyond core study VADs) for this data cut: root/clinical_studies/RO5541267/CDT30091/YO40245/data_analysis/ACE_29NOV2019/prod/outdata_vad

programs: root/clinical_studies/RO5541267/CDT30091/YO40245/data_analysis/ACE_29NOV2019/prod/program/autoexec.sas - for the subgroup definitions

root/clinical_studies/RO5541267/CDT30091/YO40245/data_analysis/ACE_Base/prod/program - note use of bubble up so same analysis is run against multiple data cuts Relevant for now is likely data_aette.sas and saf_tte.

Current tool: HEIDI to read in a modified STREAM results dataset summarizing all output content and then generate heatmaps etc to facilitate exploration of created results.

More information: https://drive.google.com/drive/u/0/folders/1FLaPNwoWbE8MC80ydad8zjodiKdo11dq

[waddella]

I will work on this for now

[yangx61]

Internally there is also standard table of similar layout, see below.

[waddella]

I have unassigned myself as I have done the discussions with gabe, @yangx61, @telepath37, @shajoezhu. I suggest @yangx61 and @shajoezhu do the following now:

• [ ] specify the derivation of each column
• [ ] list the s_* functions that already derive the content for each column
• [ ] find which derivations are missing
• [ ] create a new s_ function or extend and s_ function to have all the derivations implemented

Once done, discuss with me how to create the table.

[telepath37]

@thomas-neitmann please check if you have access to data/programs in entimice folders (see examples above) and we will discuss how to tackle this problem together with @waddella

[thomas-neitmann]

@telepath37 I can confirm that I can access the data and programs in the eICE path mentioned above.

[shajoezhu]

closing issue as it is no longer required