[Bug]: ADTTE PFS and OS (and likely the others too) are not logical

[danielinteractive]

What happened?

When working on a multi-state code template, we realized that the ADTTE data sets produced by random.cdisc.data are not logical:

1. The times between PFS and OS are not ordered logically for a single subject
2. Also the censoring indicator is not logical for a single subject

Example:

library(random.cdisc.data)
library(dplyr)
set.seed(123)
ADSL <- radsl(N = 10, seed = 1, study_duration = 2)
ADTTE <- radtte(ADSL, seed = 2)

ADTTE %>% 
  filter(PARAMCD %in% c("OS", "PFS")) %>% 
  select(SUBJID, ADY, PARAMCD, CNSR) %>% 
  filter(SUBJID == "id-5")

Here we see that this subject is censored for PFS at day 108, but has observed OS at day 81, illustrating both problems mentioned above.

sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] random.cdisc.data_0.3.13 mstate_0.3.2             survival_3.4-0           scda_0.1.6              
[5] dplyr_1.0.10            

loaded via a namespace (and not attached):
 [1] pillar_1.8.1      compiler_4.2.2    prettyunits_1.1.1 remotes_2.4.2     tools_4.2.2      
 [6] pkgbuild_1.3.1    checkmate_2.1.0   lifecycle_1.0.3   tibble_3.1.8      lattice_0.20-45  
[11] pkgconfig_2.0.3   rlang_1.0.6       Matrix_1.5-1      DBI_1.1.3         cli_3.4.0        
[16] rstudioapi_0.14   yaml_2.3.5        curl_4.3.2        withr_2.5.0       generics_0.1.3   
[21] vctrs_0.5.2       rprojroot_2.0.3   grid_4.2.2        tidyselect_1.1.2  glue_1.6.2       
[26] data.table_1.14.2 R6_2.5.1          processx_3.7.0    fansi_1.0.3       purrr_0.3.4      
[31] callr_3.7.2       magrittr_2.0.3    backports_1.4.1   ps_1.7.1          ellipsis_0.3.2   
[36] splines_4.2.2     assertthat_0.2.1  utf8_1.2.2        crayon_1.5.1

Relevant log output

# A tibble: 2 × 4
  SUBJID   ADY PARAMCD  CNSR
  <chr>  <int> <fct>   <int>
1 id-5      81 OS          0
2 id-5     108 PFS         1

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[shajoezhu]

Hi @danielinteractive , thanks for raising this, same issue with #234, some of these functions will need more refactoring, argument will need more than adsl. we will look it in more details the coming weeks

[shajoezhu]

this is linked to #13 as well

[shajoezhu]

brilliant! thanks a lot @Nolan-Steed