tern (version 0.9.8)

extract_rsp_biomarkers: Prepare response data estimates for multiple biomarkers in a single data frame

Description

Prepares estimates for number of responses, patients and overall response rate, as well as odds ratio estimates, confidence intervals and p-values, for multiple biomarkers across population subgroups in a single data frame. variables corresponds to the names of variables found in data, passed as a named list and requires elements rsp and biomarkers (vector of continuous biomarker variables) and optionally covariates, subgroups and strata. groups_lists optionally specifies groupings for subgroups variables.

Usage

extract_rsp_biomarkers(
  variables,
  data,
  groups_lists = list(),
  control = control_logistic(),
  label_all = "All Patients"
)

Value

A data.frame with columns biomarker, biomarker_label, n_tot, n_rsp, prop, or, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, and row_type.

Arguments

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.

control

(named list)
controls for the response definition and the confidence level produced by control_logistic().

label_all

(string)
label for the total population analysis.

See Also

h_logistic_mult_cont_df() which is used internally.

Examples

library(dplyr)
library(forcats)

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

adrs_f <- adrs %>%
  filter(PARAMCD == "BESRSPI") %>%
  mutate(rsp = AVALC == "CR")

# Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`,
# in logistic regression models with one covariate `RACE`. The subgroups
# are defined by the levels of `BMRKR2`.
df <- extract_rsp_biomarkers(
  variables = list(
    rsp = "rsp",
    biomarkers = c("BMRKR1", "AGE"),
    covariates = "SEX",
    subgroups = "BMRKR2"
  ),
  data = adrs_f
)
df

# Here we group the levels of `BMRKR2` manually, and we add a stratification
# variable `STRATA1`. We also here use a continuous variable `EOSDY`
# which is then binarized internally (response is defined as this variable
# being larger than 750).
df_grouped <- extract_rsp_biomarkers(
  variables = list(
    rsp = "EOSDY",
    biomarkers = c("BMRKR1", "AGE"),
    covariates = "SEX",
    subgroups = "BMRKR2",
    strata = "STRATA1"
  ),
  data = adrs_f,
  groups_lists = list(
    BMRKR2 = list(
      "low" = "LOW",
      "low/medium" = c("LOW", "MEDIUM"),
      "low/medium/high" = c("LOW", "MEDIUM", "HIGH")
    )
  ),
  control = control_logistic(
    response_definition = "I(response > 750)"
  )
)
df_grouped