Closes #63 add onco table and plot examples

[jeffreyad]

Pull Request

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[bms63]

I'm not very savvy with oncology stuff - but looks really nice from a quick glance.

maybe some folks from admiral onco team would be able to help with review - @bundfussr @pharmaverse/admiralonco any interest?

[bundfussr]

I'm not sure if the adtte_onco dataset is well suited for creating summaries. It is based on adrs_onco, which is based on rs_onco_recist. rs_onco_recist contains only eight subjects. Unfortunately, we used the complete adsl dataset when creating adrs_onco and adtte_onco. Therefore almost all patients are censored at day one, which leads to strange and highly unlikely results:

  PARAMCD PARAM                         N N_events Pct_events Median_AVAL
  <chr>   <chr>                     <int>    <int>      <dbl>       <dbl>
1 OS      Overall Survival            254        3        1.2       140  
2 PFS     Progression Free Survival   254        6        2.4         1  
3 RSD     Duration of Response          4        1       25          32.5

[rossfarrugia]

Not sure we have any other options available? Maybe this could be explained with a short note in the article?

[bundfussr]

I think for the short term we don't have other options (except maybe generating an ADTTE dataset specifically for this vignette).

In the long term we may need to revise our test data strategy. It seems that the time to load pharmaverseadam is increasing. We have observed this already in the Roche-internal syntheticadam package. Do we really need more than 300 subjects? For the ADaM websites it results in long loading times but who want to scroll through hundred of subjects in the examples? A few subjects (like in the admiralonco vignettes) to show the interesting scenarios should be sufficient. However, for TLGs it's different. Summaries with eight subjects doesn't make sense and give strange looking results.

@bms63 , @manciniedoardo , what do you think?

[bms63]

I'm not sure on the pharmaverseadam side - is there a better way to store the data? like a different format?

shall we put this in - pharmaverse/admiral#2971 ?

[manciniedoardo]

Tagging @Fanny-Gautier as the maintainer

[Fanny-Gautier]

{pharmaversesdtm} will soon be updated including .csv files. Would it be faster to also save the {pharmaverseadam} datasets as .csv?

[bundfussr]

I don't know if .csv files can be loaded faster. However, in .csv files everything is text, i.e., additional logic is required for numeric, date, datetime, and time variables. Most likely we would need metadata to load the .csv with the correct type and label.

[bms63]

is .csv something other data packages do - I have not seen that before. If we are worried about speed maybe parquet should be looked at??

[bundfussr]

CDISC recommends using values >= 1 for censoring. Currently this is not covered by Surv_CNSR() (I've created an issue suggesting to enhance it).

[bundfussr]

These labels are not displayed:

[bundfussr]

Is it possible to display the result of these calls?