SFG4

Survival Forest Graphs Within Treatment Arms by Continuous Biomarker Cutoff

SFG

We prepare the data similarly as in SFG1.

Code

library(tern)
library(dplyr)

adtte <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(
    PARAMCD == "OS",
    BEP01FL == "Y"
  ) %>%
  mutate(
    AVAL = day2month(AVAL),
    AVALU = "Months",
    is_event = CNSR == 0,
    ARM_BIN = fct_collapse_only(
      ARM,
      CTRL = "B: Placebo",
      TRT = c("A: Drug X", "C: Combination")
    )
  ) %>%
  var_relabel(
    BEP01FL = "BEP",
    BMRKR1 = "Biomarker (Countinuous)"
  )

We define a vector of all cutpoints to use for a numeric biomarker (here BMRKR1). We lapply() over this vector, each time generating a binary factor variable BMRKR1_cut and then tabulating the resulting statistics similar to SFG3, this time including the treatment arms in the subgroups argument. Then we rbind() all tables in the list together.

Code

all_cutpoints <- c(2.5, 5, 7.5, 10)

tables_all_cutpoints <- lapply(all_cutpoints, function(cutpoint) {
  adtte_cut <- adtte %>%
    mutate(
      BMRKR1_cut = explicit_na(factor(
        ifelse(BMRKR1 > cutpoint, "Greater", "Less")
      ))
    )
  tbl <- extract_survival_subgroups(
    variables = list(
      tte = "AVAL",
      is_event = "is_event",
      arm = "BMRKR1_cut",
      subgroups = "ARM_BIN"
    ),
    label_all = paste0("BMRKR1 (", cutpoint, ")"),
    data = adtte_cut
  )
  basic_table() %>%
    tabulate_survival_subgroups(
      df = tbl,
      vars = c("n_tot_events", "n", "n_events", "median", "hr", "ci"),
      time_unit = adtte_cut$AVALU[1]
    )
})

result <- do.call(rbind, tables_all_cutpoints)

We can now produce the forest plot using the g_forest() function. Similarly as in SFG3 we need to specify the col_x, col_y and forest_header arguments for g_forest() by recovering them from one of the original tables.

Code

one_table <- tables_all_cutpoints[[1]]
g_forest(
  result,
  col_x = attr(one_table, "col_x"),
  col_ci = attr(one_table, "col_ci"),
  forest_header = attr(one_table, "forest_header"),
  col_symbol_size = attr(one_table, "col_symbol_size")
)

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       rtables_0.6.9    magrittr_2.0.3  
[5] formatters_0.5.9

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0             gtable_0.3.5             jsonlite_1.8.8          
 [4] compiler_4.4.1           tidyselect_1.2.1         stringr_1.5.1           
 [7] tidyr_1.3.1              splines_4.4.1            scales_1.3.0            
[10] yaml_2.3.10              fastmap_1.2.0            lattice_0.22-6          
[13] ggplot2_3.5.1            R6_2.5.1                 labeling_0.4.3          
[16] generics_0.1.3           knitr_1.48               forcats_1.0.0           
[19] rbibutils_2.2.16         htmlwidgets_1.6.4        backports_1.5.0         
[22] checkmate_2.3.2          tibble_3.2.1             munsell_0.5.1           
[25] pillar_1.9.0             rlang_1.1.4              utf8_1.2.4              
[28] broom_1.0.6              stringi_1.8.4            xfun_0.47               
[31] cli_3.6.3                withr_3.0.1              Rdpack_2.6.1            
[34] digest_0.6.37            grid_4.4.1               cowplot_1.1.3           
[37] lifecycle_1.0.4          vctrs_0.6.5              evaluate_0.24.0         
[40] glue_1.7.0               farver_2.1.2             codetools_0.2-20        
[43] survival_3.7-0           random.cdisc.data_0.3.15 fansi_1.0.6             
[46] colorspace_2.1-1         purrr_1.0.2              rmarkdown_2.28          
[49] tools_4.4.1              pkgconfig_2.0.3          htmltools_0.5.8.1

Reuse