[Bug]: passing control_riskdiff() to riskdiff in tabulate_rsp_subgroups() and tabulate_survival_subgroups() behaves unexpectedly

[adcascone]

What happened?

Hello,

I was working through the examples included in the "Tabulate binary response by subgroup" reference site and I noticed that manipulating the pct argument in the control_riskdiff() function that is passed to the riskdiff argument of tabulate_rsp_subgroups() does not behave as expected.

Specifically, I would expect that setting pct=TRUE would return the outputs as percentages, and setting pct=FALSE would not return percentages. However, the outputs are identical regardless of whether pct is TRUE or FALSE.

Am I misguided/should the outputs above be identical? I'm seeing the same behaviors when I work through the examples in the "Tabulate survival duration by subgroup" reference site and manipulate control_riskdiff()'s arguments in the tabulate_survival_subgroups() function in a similar manner to what I've described here for tabulate_rsp_subgroups() as well.

Thank you for clarifying this!

Here is the code I ran, for replication purposes:

library(tern)
library(dplyr)
library(forcats)

adrs <- tern_ex_adrs
adrs_labels <- formatters::var_labels(adrs)

adrs_f <- adrs %>%
  filter(PARAMCD == "BESRSPI") %>%
  filter(ARM %in% c("A: Drug X", "B: Placebo")) %>%
  droplevels() %>%
  mutate(
    # Reorder levels of factor to make the placebo group the reference arm.
    ARM = fct_relevel(ARM, "B: Placebo"),
    rsp = AVALC == "CR"
  )
formatters::var_labels(adrs_f) <- c(adrs_labels, "Response")

# Unstratified analysis.
df <- extract_rsp_subgroups(
  variables = list(rsp = "rsp", arm = "ARM", subgroups = c("SEX", "BMRKR2")),
  data = adrs_f
)

basic_table() %>%
  tabulate_rsp_subgroups(
    df,
    riskdiff = control_riskdiff(
      arm_x = levels(df$prop$arm)[1],
      arm_y = levels(df$prop$arm)[2],
      pct = TRUE
    )
  )

basic_table() %>%
  tabulate_rsp_subgroups(
    df,
    riskdiff = control_riskdiff(
      arm_x = levels(df$prop$arm)[1],
      arm_y = levels(df$prop$arm)[2],
      pct = FALSE
    )
  )

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.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] forcats_1.0.0      dplyr_1.1.4        tern_0.9.6         rtables_0.6.10     magrittr_2.0.3     formatters_0.5.9  

loaded via a namespace (and not attached):
 [1] Matrix_1.7-1      gtable_0.3.6      compiler_4.4.2    tidyselect_1.2.1  tidyr_1.3.1       splines_4.4.2    
 [7] scales_1.3.0      fastmap_1.2.0     lattice_0.22-6    ggplot2_3.5.1     R6_2.5.1          generics_0.1.3   
[13] rbibutils_2.3     backports_1.5.0   checkmate_2.3.2   tibble_3.2.1      munsell_0.5.1     pillar_1.9.0     
[19] rlang_1.1.4       utf8_1.2.4        broom_1.0.7       stringi_1.8.4     cli_3.6.3         withr_2.5.2      
[25] Rdpack_2.6.1      digest_0.6.37     grid_4.4.2        rstudioapi_0.17.1 lifecycle_1.0.4   vctrs_0.6.5      
[31] glue_1.8.0        survival_3.7-0    fansi_1.0.6       colorspace_2.1-1  purrr_1.0.2       tools_4.4.2      
[37] pkgconfig_2.0.3   htmltools_0.5.8.1

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[edelarua]

Thanks for bringing this to our attention! I have opened a PR here that will fix this issue once merged in.

[adcascone]

Thank you, @edelarua!

[edelarua]

Hi @adcascone,

The fix for this issue is now available in the latest development version of tern. You can download the development version from GitHub using the following line of code:

pak::pak("insightsengineering/tern")

Thanks!

[shajoezhu]

let's revisit issue #1181 as well