R/margins.R

In tidyverse/broom: Convert Statistical Objects into Tidy Tibbles

#' @templateVar class margins
#' @template title_desc_tidy
#'
#' @param x A `margins` object returned from [margins::margins()].
#' @template param_confint
#' @template param_unused_dots
#'
#' @evalRd return_tidy(regression = TRUE)
#'
#' @details The `margins` package provides a way to obtain coefficient marginal
#'   effects for a variety of (non-linear) models, such as logit or models with
#'   multiway interaction terms. Note that the `glance.margins()` method
#'   requires rerunning the underlying model again, which can take some time.
#'   Similarly, an `augment.margins()` method is not currently supported, but
#'   users can simply run the underlying model to obtain the same information.
#'
#' @examplesIf rlang::is_installed("margins")
#'
#' # load libraries for models and data
#' library(margins)
#'
#' # example 1: logit model
#' mod_log <- glm(am ~ cyl + hp + wt, data = mtcars, family = binomial)
#'
#' # get tidied "naive" model coefficients
#' tidy(mod_log)
#'
#' # convert to marginal effects with margins()
#' marg_log <- margins(mod_log)
#'
#' # get tidied marginal effects
#' tidy(marg_log)
#' tidy(marg_log, conf.int = TRUE)
#'
#' # requires running the underlying model again. quick for this example
#' glance(marg_log)
#'
#' # augmenting `margins` outputs isn't supported, but
#' # you can get the same info by running on the underlying model
#' augment(mod_log)
#'
#' # example 2: threeway interaction terms
#' mod_ie <- lm(mpg ~ wt * cyl * disp, data = mtcars)
#'
#' # get tidied "naive" model coefficients
#' tidy(mod_ie)
#'
#' # convert to marginal effects with margins()
#' marg_ie0 <- margins(mod_ie)
#' # get tidied marginal effects
#' tidy(marg_ie0)
#' glance(marg_ie0)
#'
#' # marginal effects evaluated at specific values of a variable (here: cyl)
#' marg_ie1 <- margins(mod_ie, at = list(cyl = c(4,6,8)))
#'
#' # summarize model fit with tidiers
#' tidy(marg_ie1)
#'
#' # marginal effects of one interaction variable (here: wt), modulated at
#' # specific values of the two other interaction variables (here: cyl and drat)
#' marg_ie2 <- margins(mod_ie,
#'                     variables = "wt",
#'                     at = list(cyl = c(4,6,8), drat = c(3, 3.5, 4)))
#'
#' # summarize model fit with tidiers
#' tidy(marg_ie2)
#'
#' @export
#' @aliases margins_tidiers
#' @family margins tidiers
#' @seealso [tidy()], [margins::margins()]
tidy.margins <- function(x, conf.int = FALSE, conf.level = 0.95, ...) {
  check_ellipses("exponentiate", "tidy", "margins", ...)

  ret <- as_tibble(summary(x, level = conf.level))

  # IF statement for tidying any "at" variables.
  if ("at" %in% names(attributes(x))) {
    at_vars <- setdiff(names(attributes(x)$at), "index")
    std_cols <- c("factor", "AME", "SE", "z", "p", "lower", "upper")
    ret <-
      ret %>%
      {
        tryCatch(
          tidyr::pivot_longer(., dplyr::all_of(at_vars), names_to = "at.variable", values_to = "at.value"),
          error = function(e) {
            mutate(
              ., dplyr::across(dplyr::all_of(at_vars), as.character),
              cli::cli_warn("The {.field at.value} column was coerced to character.")
            ) %>%
              tidyr::pivot_longer(dplyr::all_of(at_vars), names_to = "at.variable", values_to = "at.value")
          }
        )
      }
  }
  # End of IF statement for tidying any "at" variables.

  # Rename and reorder variables
  ret <-
    ret %>%
    dplyr::select(
      term = factor,
      dplyr::contains("at."),
      estimate = AME,
      std.error = SE,
      statistic = z,
      p.value = p,
      conf.low = lower,
      conf.high = upper
    )

  # Remove confidence interval if not specified
  if (!conf.int) {
    ret <- dplyr::select(ret, -c(conf.low, conf.high))
  }

  # Return tidied tibble object
  return(ret)
}

#' @templateVar class margins
#' @template title_desc_glance
#'
#' @inherit tidy.margins params examples
#'
#' @evalRd return_glance(
#'   "r.squared",
#'   "adj.r.squared",
#'   "sigma",
#'   "statistic",
#'   "p.value",
#'   "df",
#'   "df.residual",
#'   "nobs"
#' )
#'
#' @export
glance.margins <- function(x, ...) {
  orig_mod_call <- attributes(x)$call
  ret <- broom::glance(eval(orig_mod_call), ...)
  return(ret)
}

#' @include null-and-default.R
#' @export
augment.margins <- augment.default