[Bug]: "label_all" dose not work in tabulate_survival_subgroups()

[fenguoerbian]

What happened?

Change label_all in tabulate_survival_subgroups() will not have any actual effect on the resulting table.

example from tabulate_survival_subgroups()'s documentation. One can see that the resulting table still has "All Patients", not "Full Analysis Set" in the first row.

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

adtte <- tern_ex_adtte

# Save variable labels before data processing steps.
adtte_labels <- formatters::var_labels(adtte)

adtte_f <- adtte %>%
    filter(
        PARAMCD == "OS",
        ARM %in% c("B: Placebo", "A: Drug X"),
        SEX %in% c("M", "F")
    ) %>%
    mutate(
        # Reorder levels of ARM to display reference arm before treatment arm.
        ARM = droplevels(fct_relevel(ARM, "B: Placebo")),
        SEX = droplevels(SEX),
        AVALU = as.character(AVALU),
        is_event = CNSR == 0
    )
labels <- c(
    "ARM" = adtte_labels[["ARM"]],
    "SEX" = adtte_labels[["SEX"]],
    "AVALU" = adtte_labels[["AVALU"]],
    "is_event" = "Event Flag"
)
formatters::var_labels(adtte_f)[names(labels)] <- labels

df <- extract_survival_subgroups(
    variables = list(
        tte = "AVAL",
        is_event = "is_event",
        arm = "ARM", subgroups = c("SEX", "BMRKR2")
    ),
    data = adtte_f
)
df

df_grouped <- extract_survival_subgroups(
    variables = list(
        tte = "AVAL",
        is_event = "is_event",
        arm = "ARM", subgroups = c("SEX", "BMRKR2")
    ),
    data = adtte_f,
    groups_lists = list(
        BMRKR2 = list(
            "low" = "LOW",
            "low/medium" = c("LOW", "MEDIUM"),
            "low/medium/high" = c("LOW", "MEDIUM", "HIGH")
        )
    )
)
df_grouped

## Table with default columns.
basic_table() %>%
    tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1], 
                                label_all = "Full Analysis Set")

sessionInfo()

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

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

other attached packages:
[1] tern_0.9.4       rtables_0.6.7    magrittr_2.0.3   formatters_0.5.6 forcats_1.0.0    dplyr_1.1.4     

loaded via a namespace (and not attached):
 [1] pillar_1.9.0      compiler_4.2.2    tools_4.2.2       digest_0.6.35     lattice_0.22-6    lifecycle_1.0.4   tibble_3.2.1     
 [8] checkmate_2.3.1   gtable_0.3.4      pkgconfig_2.0.3   rlang_1.1.3       Matrix_1.6-5      cli_3.6.2         rstudioapi_0.16.0
[15] fastmap_1.1.1     generics_0.1.3    vctrs_0.6.5       grid_4.2.2        tidyselect_1.2.1  glue_1.7.0        R6_2.5.1         
[22] fansi_1.0.6       Rdpack_2.6        survival_3.5-8    ggplot2_3.5.0     purrr_1.0.2       tidyr_1.3.1       backports_1.4.1  
[29] scales_1.3.0      htmltools_0.5.8.1 rbibutils_2.2.16  splines_4.2.2     colorspace_2.1-0  utf8_1.2.4        stringi_1.8.3    
[36] munsell_0.5.1     broom_1.0.5

Relevant log output

No response

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[edelarua]

Hi @fenguoerbian,

Sorry for the confusion in the documentation (I'll update it accordingly), the label_all parameter should actuallly be assigned in the call(s) of extract_survival_subgroups. See the updated example below:

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

adtte <- tern_ex_adtte

# Save variable labels before data processing steps.
adtte_labels <- formatters::var_labels(adtte)

adtte_f <- adtte %>%
    filter(
        PARAMCD == "OS",
        ARM %in% c("B: Placebo", "A: Drug X"),
        SEX %in% c("M", "F")
    ) %>%
    mutate(
        # Reorder levels of ARM to display reference arm before treatment arm.
        ARM = droplevels(fct_relevel(ARM, "B: Placebo")),
        SEX = droplevels(SEX),
        AVALU = as.character(AVALU),
        is_event = CNSR == 0
    )
labels <- c(
    "ARM" = adtte_labels[["ARM"]],
    "SEX" = adtte_labels[["SEX"]],
    "AVALU" = adtte_labels[["AVALU"]],
    "is_event" = "Event Flag"
)
formatters::var_labels(adtte_f)[names(labels)] <- labels

df <- extract_survival_subgroups(
    variables = list(
        tte = "AVAL",
        is_event = "is_event",
        arm = "ARM", subgroups = c("SEX", "BMRKR2")
    ),
    data = adtte_f, 
    label_all = "Full Analysis Set"
)

df_grouped <- extract_survival_subgroups(
    variables = list(
        tte = "AVAL",
        is_event = "is_event",
        arm = "ARM", subgroups = c("SEX", "BMRKR2")
    ),
    data = adtte_f,
    groups_lists = list(
        BMRKR2 = list(
            "low" = "LOW",
            "low/medium" = c("LOW", "MEDIUM"),
            "low/medium/high" = c("LOW", "MEDIUM", "HIGH")
        )
    ), 
    label_all = "Full Analysis Set"
)

## Table with default columns.
basic_table() %>%
    tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1])
#>                                                     B: Placebo               A: Drug X                                     
#> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI 
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> Full Analysis Set                  101          57         727.8         44         974.6           0.71       (0.48, 1.06)
#> Sex                                                                                                                        
#>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96)
#>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65)
#> Continuous Level Biomarker 2                                                                                               
#>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51)
#>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61)
#>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)

^{Created on 2024-04-19 with reprex v2.1.0}

[fenguoerbian]

Thanks a lot!