h_survival_duration_subgroups: Helper functions for tabulating survival duration by subgroup

In tern: Create Common TLGs Used in Clinical Trials

Helper functions for tabulating survival duration by subgroup

Description

Helper functions that tabulate in a data frame statistics such as median survival time and hazard ratio for population subgroups.

Usage

h_survtime_df(tte, is_event, arm)

h_survtime_subgroups_df(
  variables,
  data,
  groups_lists = list(),
  label_all = "All Patients"
)

h_coxph_df(tte, is_event, arm, strata_data = NULL, control = control_coxph())

h_coxph_subgroups_df(
  variables,
  data,
  groups_lists = list(),
  control = control_coxph(),
  label_all = "All Patients"
)

Arguments

tte	(numeric) vector of time-to-event duration values.
is_event	(flag) TRUE if event, FALSE if time to event is censored.
arm	(factor) the treatment group variable.
variables	(named list of string) list of additional analysis variables.
data	(data.frame) the dataset containing the variables to summarize.
groups_lists	(named list of list) optionally contains for each subgroups variable a list, which specifies the new group levels via the names and the levels that belong to it in the character vectors that are elements of the list.
label_all	(string) label for the total population analysis.
strata_data	(factor, data.frame, or NULL) required if stratified analysis is performed.
control	(list) parameters for comparison details, specified by using the helper function control_coxph(). Some possible parameter options are: pval_method (string) p-value method for testing the null hypothesis that hazard ratio = 1. Default method is "log-rank" which comes from survival::survdiff(), can also be set to "wald" or "likelihood" (from survival::coxph()). ties (string) specifying the method for tie handling. Default is "efron", can also be set to "breslow" or "exact". See more in survival::coxph(). conf_level (proportion) confidence level of the interval for HR.

Details

Main functionality is to prepare data for use in a layout-creating function.

Value

• h_survtime_df() returns a data.frame with columns arm, n, n_events, and median.

• h_survtime_subgroups_df() returns a data.frame with columns arm, n, n_events, median, subgroup, var, var_label, and row_type.

• h_coxph_df() returns a data.frame with columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval and pval_label.

• h_coxph_subgroups_df() returns a data.frame with columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, and row_type.

Functions

• h_survtime_df(): Helper to prepare a data frame of median survival times by arm.

• h_survtime_subgroups_df(): Summarizes median survival times by arm and across subgroups in a data frame. variables corresponds to the names of variables found in data, passed as a named list and requires elements tte, is_event, arm and optionally subgroups. groups_lists optionally specifies groupings for subgroups variables.

• h_coxph_df(): Helper to prepare a data frame with estimates of treatment hazard ratio.

• h_coxph_subgroups_df(): Summarizes estimates of the treatment hazard ratio across subgroups in a data frame. variables corresponds to the names of variables found in data, passed as a named list and requires elements tte, is_event, arm and optionally subgroups and strata. groups_lists optionally specifies groupings for subgroups variables.

Examples

library(dplyr)
library(forcats)

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),
    is_event = CNSR == 0
  )
labels <- c("ARM" = adtte_labels[["ARM"]], "SEX" = adtte_labels[["SEX"]], "is_event" = "Event Flag")
formatters::var_labels(adtte_f)[names(labels)] <- labels

# Extract median survival time for one group.
h_survtime_df(
  tte = adtte_f$AVAL,
  is_event = adtte_f$is_event,
  arm = adtte_f$ARM
)

# Extract median survival time for multiple groups.
h_survtime_subgroups_df(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM",
    subgroups = c("SEX", "BMRKR2")
  ),
  data = adtte_f
)

# Define groupings for BMRKR2 levels.
h_survtime_subgroups_df(
  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")
    )
  )
)

# Extract hazard ratio for one group.
h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM)

# Extract hazard ratio for one group with stratification factor.
h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM, strata_data = adtte_f$STRATA1)

# Extract hazard ratio for multiple groups.
h_coxph_subgroups_df(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM",
    subgroups = c("SEX", "BMRKR2")
  ),
  data = adtte_f
)

# Define groupings of BMRKR2 levels.
h_coxph_subgroups_df(
  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")
    )
  )
)

# Extract hazard ratio for multiple groups with stratification factors.
h_coxph_subgroups_df(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM",
    subgroups = c("SEX", "BMRKR2"),
    strata = c("STRATA1", "STRATA2")
  ),
  data = adtte_f
)

tern documentation built on Sept. 24, 2024, 9:06 a.m.