TET1A

Time-to-Event Summary Table with Stratified Analysis

We will use the cadtte data set from the random.cdisc.data package for the time-to-event summary table. We start by filtering the adtte data set for the overall survival observations, converting time of overall survival to months, creating new variables for event and non-event information and binarizing the ARM variable.

Code

library(tern)
library(dplyr)

adtte <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(
    PARAMCD == "OS"
  ) %>%
  mutate(
    AVAL = day2month(AVAL),
    AVALU = "Months",
    is_event = CNSR == 0,
    is_not_event = CNSR == 1,
    ARM_BIN = fct_collapse_only(
      ARM,
      CTRL = c("B: Placebo"),
      TRT = c("A: Drug X", "C: Combination")
    )
  )

We can add the summary of an analysis with Cox Proportional Hazards models stratified by SEX to the table above using coxph_pairwise().

Code

lyt <- basic_table() %>%
  split_cols_by(
    var = "ARM_BIN",
    ref_group = "CTRL"
  ) %>%
  add_colcounts() %>%
  analyze_vars(
    vars = "is_event",
    .stats = "count_fraction",
    .labels = c(count_fraction = "Patients with event (%)"),
    nested = FALSE,
    show_labels = "hidden"
  ) %>%
  analyze_vars(
    vars = "is_not_event",
    .stats = "count_fraction",
    .labels = c(count_fraction = "Patients without event (%)"),
    nested = FALSE,
    show_labels = "hidden"
  ) %>%
  surv_time(
    vars = "AVAL",
    var_labels = "Time to Event (months)",
    is_event = "is_event",
    table_names = "time_to_event"
  ) %>%
  coxph_pairwise(
    vars = "AVAL",
    is_event = "is_event",
    var_labels = c("Unstratified Analysis"),
    control = control_coxph(pval_method = "log-rank"),
    table_names = "coxph_unstratified"
  )
lyt2 <- lyt %>%
  coxph_pairwise(
    vars = "AVAL",
    is_event = "is_event",
    var_labels = c("Stratified Analysis"),
    strat = "SEX",
    control = control_coxph(pval_method = "log-rank"),
    table_names = "coxph_stratified"
  )

build_table(lyt2, adtte)

                                  CTRL               TRT      
                                 (N=134)           (N=266)    
——————————————————————————————————————————————————————————————
Patients with event (%)        58 (43.3%)        127 (47.7%)  
Patients without event (%)     76 (56.7%)        139 (52.3%)  
Time to Event (months)                                        
  Median                           NA                NA       
    95% CI                      (9.4, NA)         (9.2, NA)   
  25% and 75%-ile                5.6, NA           5.4, NA    
  Range                      0.9 to 16.3 {1}   0.5 to 16.4 {1}
Unstratified Analysis                                         
  p-value (log-rank)                               0.4068     
  Hazard Ratio                                      1.14      
  95% CI                                        (0.84, 1.56)  
Stratified Analysis                                           
  p-value (log-rank)                               0.4243     
  Hazard Ratio                                      1.13      
  95% CI                                        (0.83, 1.55)  
——————————————————————————————————————————————————————————————

{1} - Censored observation: range maximum
——————————————————————————————————————————————————————————————

Code

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] dplyr_1.1.4       tern_0.9.7        rtables_0.6.11    magrittr_2.0.3   
[5] formatters_0.5.10

loaded via a namespace (and not attached):
 [1] Matrix_1.7-2             gtable_0.3.6             jsonlite_1.9.0          
 [4] compiler_4.4.2           tidyselect_1.2.1         stringr_1.5.1           
 [7] tidyr_1.3.1              splines_4.4.2            scales_1.3.0            
[10] yaml_2.3.10              fastmap_1.2.0            lattice_0.22-6          
[13] ggplot2_3.5.1            R6_2.6.1                 generics_0.1.3          
[16] knitr_1.49               forcats_1.0.0            rbibutils_2.3           
[19] htmlwidgets_1.6.4        backports_1.5.0          checkmate_2.3.2         
[22] tibble_3.2.1             munsell_0.5.1            pillar_1.10.1           
[25] rlang_1.1.5              broom_1.0.7              stringi_1.8.4           
[28] xfun_0.51                cli_3.6.4                Rdpack_2.6.2            
[31] digest_0.6.37            grid_4.4.2               lifecycle_1.0.4         
[34] vctrs_0.6.5              evaluate_1.0.3           glue_1.8.0              
[37] nestcolor_0.1.3          codetools_0.2-20         survival_3.8-3          
[40] random.cdisc.data_0.3.16 colorspace_2.1-1         rmarkdown_2.29          
[43] purrr_1.0.4              tools_4.4.2              pkgconfig_2.0.3         
[46] htmltools_0.5.8.1

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