Draft Example data sets

bailliem commented 2 years ago

I have added a draft data set (ADTTE again) I simulated a while ago. This time ADTTE is based on a trial in breast cancer comparing 4 different treatment regimens. See here for background.

library(ggsurvfit)
library(ggplot2)
p <- ADTTE %>%  survfit2(Surv(AVAL, 1-CNSR) ~ TRT01P, data = .) %>%
  ggsurvfit() +
  add_censor_mark() +
  add_confidence_interval() 

p
p + add_risktable()

It does provide challenges with the treatment labels and the number of arms. The treatment labels, etc. could all be edited.

The data set and variable definitions

The data set is an abridged version of the CDISC ADaM ADTTE time to event data set.

The data set contains the following variables:

STUDYID - the study identifier
SUBJID - subject identifier
USUBJID - unique subject iddentifier
AGE - age at randomisation (years)
STR01 - Hormone receptor status at randomisation
STR01N - Hormone receptor positive (Numeric)
STR01L - Hormone receptor positive (Long format)
STR02 - Prior Radiotherapy at randomisation
STR02N - Prior Radiotherapy at randomisation (Numeric)
STR02L - Prior Radiotherapy at randomisation (Long format)
TRT01P - Planned treatment assigned at randomisation
TRT01PN - Planned treatment assigned at randomisation (Numeric)
PARAM - Analysis parameter - Progression free survival
PARAMCD - Analysis parameter code
AVAL - Analysis value (time to event [days])
CNSR - Censoring (0 = Event, 1 = censored)
EVNTDESC - Event description
CNSDTDSC - Censoring description
DCTREAS - Discontinuation from study reason

A number of baseline measurements are also included such as age, hormone receptor status and prior radiotherapy treatment. Additional details on reasons for study discontinuation and censoring event description are also included.

ddsjoberg commented 2 years ago

Fantastic! I'm working on a theme that replaces the strata labels with a block of color in the risk tables. I think that will alleviate many of the concerns from long labels.

I think I've found a solution (somewhat fiddly), and it needs testing to see how it holds up against users' customizations....

ddsjoberg commented 2 years ago

@bailliem how do you want to deal with the CNSR coding in this dataset? Just pass Surv(AVAL, 1 - CNSR)?

bailliem commented 2 years ago

@bailliem how do you want to deal with the CNSR coding in this dataset? Just pass Surv(AVAL, 1 - CNSR)?

I think so for now. Could also have an example which demostrates the Surv_CNSR function. But to be discussed..

bailliem commented 2 years ago

This will be a great addition.

[x] can you add column labels to the data frame?

[x] the data set needs to be documented in the R/data.R file.

[x] do you think it would be worth it to include the simulation code in data-raw/DATASETS.R ?

ping - can you take a look now. Source data is in there but sharing simulation code may be tricky.

pharmaverse / ggsurvfit

Draft Example data sets #33

The data set and variable definitions