TET1A

Time-to-Event Summary Table with Stratified Analysis

TET

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 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 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-r0.3.20.so;  LAPACK version 3.10.0

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_0.9.5.9022       rtables_0.6.9.9014   
[4] magrittr_2.0.3        formatters_0.5.9.9001

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0                  gtable_0.3.5                 
 [3] jsonlite_1.8.8                compiler_4.4.1               
 [5] tidyselect_1.2.1              stringr_1.5.1                
 [7] tidyr_1.3.1                   splines_4.4.1                
 [9] scales_1.3.0                  yaml_2.3.10                  
[11] fastmap_1.2.0                 lattice_0.22-6               
[13] ggplot2_3.5.1                 R6_2.5.1                     
[15] generics_0.1.3                knitr_1.48                   
[17] forcats_1.0.0                 rbibutils_2.2.16             
[19] htmlwidgets_1.6.4             backports_1.5.0              
[21] checkmate_2.3.2               tibble_3.2.1                 
[23] munsell_0.5.1                 pillar_1.9.0                 
[25] rlang_1.1.4                   utf8_1.2.4                   
[27] broom_1.0.6                   stringi_1.8.4                
[29] xfun_0.47                     cli_3.6.3                    
[31] Rdpack_2.6.1                  digest_0.6.37                
[33] grid_4.4.1                    lifecycle_1.0.4              
[35] vctrs_0.6.5                   evaluate_0.24.0              
[37] glue_1.7.0                    codetools_0.2-20             
[39] survival_3.7-0                random.cdisc.data_0.3.15.9009
[41] fansi_1.0.6                   colorspace_2.1-1             
[43] purrr_1.0.2                   rmarkdown_2.28               
[45] tools_4.4.1                   pkgconfig_2.0.3              
[47] htmltools_0.5.8.1

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