KG1A

Kaplan-Meier Graph for Biomarker Evaluable Population in One Treatment Arm

We will use the cadtte data set from the random.cdisc.data package to create the Kaplan-Meier (KM) plots. We start by filtering the time-to-event dataset for the overall survival observations and by one treatment arm (A), creating a new variable for event information, and curating a list of variables required to produce the plot.

Code

library(tern)
library(dplyr)
library(ggplot2)
library(grid)

adtte_arm <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(PARAMCD == "OS", ARM == "A: Drug X") %>%
  mutate(is_event = CNSR == 0)

variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM")

We can filter the dataset further for the biomarker evaluable population using the corresponding flag variable, here BEP01FL:

Code

adtte_arm_bep <- adtte_arm %>%
  filter(BEP01FL == "Y")

Afterwards we can plot the basic KM graph, just using the further filtered dataset adtte_bep. Here we annotate the plot with median survival time, but could suppress it with annot_surv_med = FALSE.

Code

g_km(
  df = adtte_arm_bep,
  variables = variables,
  annot_surv_med = TRUE,
  rel_height_plot = 0.85
)

Code

sessionInfo()

R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 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-r0.3.26.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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ggplot2_4.0.2     dplyr_1.2.1       tern_0.9.10       rtables_0.6.15   
[5] magrittr_2.0.5    formatters_0.5.12

loaded via a namespace (and not attached):
 [1] generics_0.1.4           tidyr_1.3.2              stringi_1.8.7           
 [4] lattice_0.22-9           digest_0.6.39            evaluate_1.0.5          
 [7] RColorBrewer_1.1-3       fastmap_1.2.0            jsonlite_2.0.0          
[10] Matrix_1.7-5             backports_1.5.1          survival_3.8-6          
[13] purrr_1.2.1              scales_1.4.0             codetools_0.2-20        
[16] Rdpack_2.6.6             cli_3.6.5                nestcolor_0.1.3         
[19] rlang_1.2.0              rbibutils_2.4.1          cowplot_1.2.0           
[22] splines_4.5.2            withr_3.0.2              yaml_2.3.12             
[25] otel_0.2.0               tools_4.5.2              checkmate_2.3.4         
[28] forcats_1.0.1            broom_1.0.12             vctrs_0.7.2             
[31] R6_2.6.1                 lifecycle_1.0.5          stringr_1.6.0           
[34] htmlwidgets_1.6.4        pkgconfig_2.0.3          pillar_1.11.1           
[37] gtable_0.3.6             glue_1.8.0               xfun_0.57               
[40] tibble_3.3.1             tidyselect_1.2.1         knitr_1.51              
[43] dichromat_2.0-0.1        farver_2.1.2             htmltools_0.5.9         
[46] rmarkdown_2.31           labeling_0.4.3           random.cdisc.data_0.3.16
[49] compiler_4.5.2           S7_0.2.1

Reuse