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Custom Tidy Method for Binomial GLM Results

Source: R/logistic_regression.R
tidy.glm.Rd

[Stable]

Helper method (for broom::tidy()) to prepare a data frame from a glm object with binomial family.

Usage 

# S3 method for glm
tidy(fit_glm, conf_level = 0.95, at = NULL)

Arguments

fit_glm

logistic regression model fitted by stats::glm() with "binomial" family.

conf_level

(proportion)
confidence level of the interval.

at

(NULL or numeric)
optional values for the interaction variable. Otherwise the median is used.

Value

A data.frame containing the tidied model.

See also

h_logistic_regression for relevant helper functions.

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")
  )
)
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
mod2 <- fit_logistic(
  data = adrs_f,
  variables = list(
    response = "Response",
    arm = "ARMCD",
    covariates = c("AGE", "RACE"),
    interaction = "AGE"
  )
)
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred

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