tidy_add_pairwise_contrasts: Add pairwise contrasts for categorical variables

In larmarange/broom.helpers: Helpers for Model Coefficients Tibbles

Add pairwise contrasts for categorical variables

Description

Computes pairwise contrasts with emmeans::emmeans() and add them to the results tibble. Works only with models supported by emmeans, see vignette("models", package = "emmeans").

Usage

tidy_add_pairwise_contrasts(
  x,
  variables = all_categorical(),
  keep_model_terms = FALSE,
  pairwise_reverse = TRUE,
  contrasts_adjust = NULL,
  conf.level = attr(x, "conf.level"),
  emmeans_args = list(),
  model = tidy_get_model(x),
  quiet = FALSE
)

Arguments

x	(data.frame) A tidy tibble as produced by ⁠tidy_*()⁠ functions.
variables	include (tidy-select) Variables for those pairwise contrasts should be added. Default is all_categorical().
keep_model_terms	(logical) Keep terms from the model?
pairwise_reverse	(logical) Determines whether to use "pairwise" (if TRUE) or "revpairwise" (if FALSE), see emmeans::contrast().
contrasts_adjust	(string) Optional adjustment method when computing contrasts, see emmeans::contrast() (if NULL, use emmeans default).
conf.level	(numeric) Confidence level, by default use the value indicated previously in tidy_and_attach().
emmeans_args	(list) List of additional parameter to pass to emmeans::emmeans() when computing pairwise contrasts.
model	(a model object, e.g. glm) The corresponding model, if not attached to x.
quiet	(logical) Whether broom.helpers should not return a message when requested output cannot be generated. Default is FALSE.

Note

If the contrasts column is not yet available in x, tidy_add_contrasts() will be automatically applied.

For multi-components models, such as zero-inflated Poisson or beta regression, support of pairwise contrasts is still experimental.

See Also

Other tidy_helpers: tidy_add_coefficients_type(), tidy_add_contrasts(), tidy_add_estimate_to_reference_rows(), tidy_add_header_rows(), tidy_add_n(), tidy_add_reference_rows(), tidy_add_term_labels(), tidy_add_variable_labels(), tidy_attach_model(), tidy_disambiguate_terms(), tidy_identify_variables(), tidy_plus_plus(), tidy_remove_intercept(), tidy_select_variables()

Examples

if (.assert_package("emmeans", boolean = TRUE)) {
  mod1 <- lm(Sepal.Length ~ Species, data = iris)
  mod1 |>
    tidy_and_attach() |>
    tidy_add_pairwise_contrasts()

  mod1 |>
    tidy_and_attach() |>
    tidy_add_pairwise_contrasts(pairwise_reverse = FALSE)

  mod1 |>
    tidy_and_attach() |>
    tidy_add_pairwise_contrasts(keep_model_terms = TRUE)

  mod1 |>
    tidy_and_attach() |>
    tidy_add_pairwise_contrasts(contrasts_adjust = "none")

  if (.assert_package("gtsummary", boolean = TRUE)) {
    mod2 <- glm(
      response ~ age + trt + grade,
      data = gtsummary::trial,
      family = binomial
    )
    mod2 |>
      tidy_and_attach(exponentiate = TRUE) |>
      tidy_add_pairwise_contrasts()
  }
}

larmarange/broom.helpers documentation built on Sept. 27, 2024, 12:35 a.m.