inst/doc/introduction_comparisons_3.R

In modelbased: Estimation of Model-Based Predictions, Contrasts and Means

## ----set-options, echo = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  dev = "png",
  fig.width = 7,
  fig.height = 3.5,
  message = FALSE, warning = FALSE
)
options(width = 800)
arrow_color <- "#FF00cc"
p <- ht8 <- NULL

pkgs <- c("ggplot2", "see", "marginaleffects")

if (!all(vapply(pkgs, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1L)))) {
  knitr::opts_chunk$set(eval = FALSE)
}

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(modelbased)
set.seed(1234)
dat <- data.frame(
  outcome = rbinom(n = 100, size = 1, prob = 0.35),
  x1 = as.factor(sample(1:3, size = 100, TRUE, prob = c(0.5, 0.2, 0.3))),
  x2 = rnorm(n = 100, mean = 10, sd = 7),
  x3 = as.factor(sample(1:4, size = 100, TRUE, prob = c(0.1, 0.4, 0.2, 0.3)))
)

m <- glm(outcome ~ x1 + x2 + x3, data = dat, family = binomial())
estimate_means(m, "x1")

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
estimate_contrasts(m, "x1")

## ----echo=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
p <- estimate_means(m, "x1")
ht8 <- estimate_contrasts(m, "x1")

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
estimate_contrasts(m, "x1", predict = "link")

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
estimate_contrasts(m, "x1", predict = "link", transform = exp)