tern (version 0.9.8)

h_survival_biomarkers_subgroups: Helper functions for tabulating biomarker effects on survival by subgroup

Description

Helper functions which are documented here separately to not confuse the user when reading about the user-facing functions.

Usage

h_surv_to_coxreg_variables(variables, biomarker)
h_coxreg_mult_cont_df(variables, data, control = control_coxreg())

Value

• h_surv_to_coxreg_variables() returns a named list of elements time, event, arm, covariates, and strata.

• h_coxreg_mult_cont_df() returns a data.frame containing estimates and statistics for the selected biomarkers.

Arguments

variables

(named list of string)
list of additional analysis variables.

biomarker

(string)
the name of the biomarker variable.

data

(data.frame)
the dataset containing the variables to summarize.

control

(list)
a list of parameters as returned by the helper function control_coxreg().

Functions

• h_surv_to_coxreg_variables(): Helps with converting the "survival" function variable list to the "Cox regression" variable list. The reason is that currently there is an inconsistency between the variable names accepted by extract_survival_subgroups() and fit_coxreg_multivar().

• h_coxreg_mult_cont_df(): Prepares estimates for number of events, patients and median survival times, as well as hazard ratio estimates, confidence intervals and p-values, for multiple biomarkers in a given single data set. variables corresponds to names of variables found in data, passed as a named list and requires elements tte, is_event, biomarkers (vector of continuous biomarker variables) and optionally subgroups and strata.

Examples

library(dplyr)
library(forcats)

adtte <- tern_ex_adtte

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

adtte_f <- adtte %>%
  filter(PARAMCD == "OS") %>%
  mutate(
    AVALU = as.character(AVALU),
    is_event = CNSR == 0
  )
labels <- c("AVALU" = adtte_labels[["AVALU"]], "is_event" = "Event Flag")
formatters::var_labels(adtte_f)[names(labels)] <- labels

# This is how the variable list is converted internally.
h_surv_to_coxreg_variables(
  variables = list(
    tte = "AVAL",
    is_event = "EVNT",
    covariates = c("A", "B"),
    strata = "D"
  ),
  biomarker = "AGE"
)

# For a single population, estimate separately the effects
# of two biomarkers.
df <- h_coxreg_mult_cont_df(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    biomarkers = c("BMRKR1", "AGE"),
    covariates = "SEX",
    strata = c("STRATA1", "STRATA2")
  ),
  data = adtte_f
)
df

# If the data set is empty, still the corresponding rows with missings are returned.
h_coxreg_mult_cont_df(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    biomarkers = c("BMRKR1", "AGE"),
    covariates = "REGION1",
    strata = c("STRATA1", "STRATA2")
  ),
  data = adtte_f[NULL, ]
)