summarize_logistic: Multivariate logistic regression table

In tern: Create Common TLGs Used in Clinical Trials

Multivariate logistic regression table

Description

Layout-creating function which summarizes a logistic variable regression for binary outcome with categorical/continuous covariates in model statement. For each covariate category (if categorical) or specified values (if continuous), present degrees of freedom, regression parameter estimate and standard error (SE) relative to reference group or category. Report odds ratios for each covariate category or specified values and corresponding Wald confidence intervals as default but allow user to specify other confidence levels. Report p-value for Wald chi-square test of the null hypothesis that covariate has no effect on response in model containing all specified covariates. Allow option to include one two-way interaction and present similar output for each interaction degree of freedom.

Usage

summarize_logistic(
  lyt,
  conf_level,
  drop_and_remove_str = "",
  .indent_mods = NULL
)

Arguments

lyt	(PreDataTableLayouts) layout that analyses will be added to.
conf_level	(proportion) confidence level of the interval.
drop_and_remove_str	(string) string to be dropped and removed.
.indent_mods	(named integer) indent modifiers for the labels. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.

Value

A layout object suitable for passing to further layouting functions, or to rtables::build_table(). Adding this function to an rtable layout will add a logistic regression variable summary to the table layout.

Note

For the formula, the variable names need to be standard data.frame column names without special characters.

Examples

library(dplyr)
library(broom)

adrs_f <- tern_ex_adrs %>%
  filter(PARAMCD == "BESRSPI") %>%
  filter(RACE %in% c("ASIAN", "WHITE", "BLACK OR AFRICAN AMERICAN")) %>%
  mutate(
    Response = case_when(AVALC %in% c("PR", "CR") ~ 1, TRUE ~ 0),
    RACE = factor(RACE),
    SEX = factor(SEX)
  )
formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = "Response")
mod1 <- fit_logistic(
  data = adrs_f,
  variables = list(
    response = "Response",
    arm = "ARMCD",
    covariates = c("AGE", "RACE")
  )
)
mod2 <- fit_logistic(
  data = adrs_f,
  variables = list(
    response = "Response",
    arm = "ARMCD",
    covariates = c("AGE", "RACE"),
    interaction = "AGE"
  )
)

df <- tidy(mod1, conf_level = 0.99)
df2 <- tidy(mod2, conf_level = 0.99)

# flagging empty strings with "_"
df <- df_explicit_na(df, na_level = "_")
df2 <- df_explicit_na(df2, na_level = "_")

result1 <- basic_table() %>%
  summarize_logistic(
    conf_level = 0.95,
    drop_and_remove_str = "_"
  ) %>%
  build_table(df = df)
result1

result2 <- basic_table() %>%
  summarize_logistic(
    conf_level = 0.95,
    drop_and_remove_str = "_"
  ) %>%
  build_table(df = df2)
result2

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