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This alias is kept for backward compatibility and because some users may prefer that name.

Usage

marginalmeans(
  model,
  variables = NULL,
  variables_grid = NULL,
  vcov = TRUE,
  conf_level = 0.95,
  type = NULL,
  transform_post = NULL,
  cross = FALSE,
  hypothesis = NULL,
  df = Inf,
  wts = "equal",
  by = NULL,
  ...
)

Arguments

model

Model object

variables

character vector Categorical predictors over which to compute marginal means. NULL calculates marginal means for all logical, character, or factor variables in the dataset used to fit model. Set cross=TRUE to compute marginal means at combinations of the predictors specified in the variables argument.

variables_grid

character vector Categorical predictors used to construct the prediction grid over which adjusted predictions are averaged (character vector). NULL creates a grid with all combinations of all categorical predictors. This grid can be very large when there are many variables and many response levels, so it is advisable to select a limited number of variables in the variables and variables_grid arguments.

vcov

Type of uncertainty estimates to report (e.g., for robust standard errors). Acceptable values:

  • FALSE: Do not compute standard errors. This can speed up computation considerably.

  • TRUE: Unit-level standard errors using the default vcov(model) variance-covariance matrix.

  • String which indicates the kind of uncertainty estimates to return.

    • Heteroskedasticity-consistent: "HC", "HC0", "HC1", "HC2", "HC3", "HC4", "HC4m", "HC5". See ?sandwich::vcovHC

    • Heteroskedasticity and autocorrelation consistent: "HAC"

    • Mixed-Models degrees of freedom: "satterthwaite", "kenward-roger"

    • Other: "NeweyWest", "KernHAC", "OPG". See the sandwich package documentation.

  • One-sided formula which indicates the name of cluster variables (e.g., ~unit_id). This formula is passed to the cluster argument of the sandwich::vcovCL function.

  • Square covariance matrix

  • Function which returns a covariance matrix (e.g., stats::vcov(model))

conf_level

numeric value between 0 and 1. Confidence level to use to build a confidence interval.

type

string indicates the type (scale) of the predictions used to compute marginal effects or contrasts. This can differ based on the model type, but will typically be a string such as: "response", "link", "probs", or "zero". When an unsupported string is entered, the model-specific list of acceptable values is returned in an error message. When type is NULL, the default value is used. This default is the first model-related row in the marginaleffects:::type_dictionary dataframe. If type is NULL and the default value is "response", the function tries to compute marginal means on the link scale before backtransforming them using the inverse link function.

transform_post

(experimental) A function applied to unit-level adjusted predictions and confidence intervals just before the function returns results. For bayesian models, this function is applied to individual draws from the posterior distribution, before computing summaries.

cross

TRUE or FALSE

  • FALSE (default): Marginal means are computed for each predictor individually.

  • TRUE: Marginal means are computed for each combination of predictors specified in the variables argument.

hypothesis

specify a hypothesis test or custom contrast using a numeric value, vector, or matrix, a string, or a string formula.

  • Numeric:

    • Single value: the null hypothesis used in the computation of Z and p (before applying transform_post).

    • Vector: Weights to compute a linear combination of (custom contrast between) estimates. Length equal to the number of rows generated by the same function call, but without the hypothesis argument.

    • Matrix: Each column is a vector of weights, as describe above, used to compute a distinct linear combination of (contrast between) estimates. The column names of the matrix are used as labels in the output.

  • String formula to specify linear or non-linear hypothesis tests. If the term column uniquely identifies rows, terms can be used in the formula. Otherwise, use b1, b2, etc. to identify the position of each parameter. Examples:

    • hp = drat

    • hp + drat = 12

    • b1 + b2 + b3 = 0

  • String:

    • "pairwise": pairwise differences between estimates in each row.

    • "reference": differences between the estimates in each row and the estimate in the first row.

    • "sequential": difference between an estimate and the estimate in the next row.

    • "revpairwise", "revreference", "revsequential": inverse of the corresponding hypotheses, as described above.

  • See the Examples section below and the vignette: https://vincentarelbundock.github.io/marginaleffects/articles/hypothesis.html

df

Degrees of freedom used to compute p values and confidence intervals. A single numeric value between 1 and Inf. When df is Inf, the normal distribution is used. When df is finite, the t distribution is used. See insight::get_df for a convenient function to extract degrees of freedom. Ex: slopes(model, df = insight::get_df(model))

wts

character value. Weights to use in the averaging.

  • "equal": each combination of variables in variables_grid gets an equal weight.

  • "cells": each combination of values for the variables in the variables_grid gets a weight proportional to its frequency in the original data.

  • "proportional": each combination of values for the variables in the variables_grid -- except for those in the variables argument -- gets a weight proportional to its frequency in the original data.

by

Collapse marginal means into categories. Data frame with a by column of group labels, and merging columns shared by newdata or the data frame produced by calling the same function without the by argument.

...

Additional arguments are passed to the predict() method supplied by the modeling package.These arguments are particularly useful for mixed-effects or bayesian models (see the online vignettes on the marginaleffects website). Available arguments can vary from model to model, depending on the range of supported arguments by each modeling package. See the "Model-Specific Arguments" section of the ?marginaleffects documentation for a non-exhaustive list of available arguments.

Value

Data frame of marginal means with one row per variable-value combination.

Details

This function begins by calling the predictions function to obtain a grid of predictors, and adjusted predictions for each cell. The grid includes all combinations of the categorical variables listed in the variables and variables_grid arguments, or all combinations of the categorical variables used to fit the model if variables_grid is NULL. In the prediction grid, numeric variables are held at their means.

After constructing the grid and filling the grid with adjusted predictions, marginal_means computes marginal means for the variables listed in the variables argument, by average across all categories in the grid.

marginal_means can only compute standard errors for linear models, or for predictions on the link scale, that is, with the type argument set to "link".

The marginaleffects website compares the output of this function to the popular emmeans package, which provides similar but more advanced functionality: https://vincentarelbundock.github.io/marginaleffects/

Model-Specific Arguments

Some model types allow model-specific arguments to modify the nature of marginal effects, predictions, marginal means, and contrasts.

PackageClassArgumentDocumentation
brmsbrmsfitndrawsbrms::posterior_predict
re_formula
lme4merModinclude_randominsight::get_predicted
re.formlme4::predict.merMod
allow.new.levelslme4::predict.merMod
glmmTMBglmmTMBre.formglmmTMB::predict.glmmTMB
allow.new.levelsglmmTMB::predict.glmmTMB
zitypeglmmTMB::predict.glmmTMB
mgcvbamexcludemgcv::predict.bam
robustlmmrlmerModre.formrobustlmm::predict.rlmerMod
allow.new.levelsrobustlmm::predict.rlmerMod

Bayesian posterior summaries

By default, credible intervals in bayesian models are built as equal-tailed intervals. This can be changed to a highest density interval by setting a global option:

options("marginaleffects_posterior_interval" = "eti")

options("marginaleffects_posterior_interval" = "hdi")

By default, the center of the posterior distribution in bayesian models is identified by the median. Users can use a different summary function by setting a global option:

options("marginaleffects_posterior_center" = "mean")

options("marginaleffects_posterior_center" = "median")

When estimates are averaged using the by argument, the tidy() function, or the summary() function, the posterior distribution is marginalized twice over. First, we take the average across units but within each iteration of the MCMC chain, according to what the user requested in by argument or tidy()/summary() functions. Then, we identify the center of the resulting posterior using the function supplied to the "marginaleffects_posterior_center" option (the median by default).

Examples

library(marginaleffects)

# simple marginal means for each level of `cyl`
dat <- mtcars
dat$carb <- factor(dat$carb)
dat$cyl <- factor(dat$cyl)
dat$am <- as.logical(dat$am)
mod <- lm(mpg ~ carb + cyl + am, dat)

marginal_means(
  mod,
  variables = "cyl")
#> Error: Elements of the `variables` argument were not found as column names in
#>   the data used to fit the model: cyl

# collapse levels of cyl by averaging
by <- data.frame(
  cyl = c(4, 6, 8),
  by = c("4 & 6", "4 & 6", "8"))
marginal_means(mod,
  variables = "cyl",
  by = by)
#> Error: The `by` argument must be either:
#>   
#>   1. Character vector in which each element is part of: Package, Function,
#>   dydx, se, stata_dydx, stata_se, margins_dydx, margins_se, emmeans_dydx,
#>   emmeans_se
#>   
#>   2. A data frame with a `by` column of labels, and in which all other
#>   columns are elements of: Package, Function, dydx, se, stata_dydx,
#>   stata_se, margins_dydx, margins_se, emmeans_dydx, emmeans_se
#>   
#>   It can sometimes be useful to supply a data frame explicitly to the
#>   `newdata` argument in order to be able to group by different columns.

# pairwise differences between collapsed levels
marginal_means(mod,
  variables = "cyl",
  by = by,
  hypothesis = "pairwise")
#> Error: The `by` argument must be either:
#>   
#>   1. Character vector in which each element is part of: Package, Function,
#>   dydx, se, stata_dydx, stata_se, margins_dydx, margins_se, emmeans_dydx,
#>   emmeans_se
#>   
#>   2. A data frame with a `by` column of labels, and in which all other
#>   columns are elements of: Package, Function, dydx, se, stata_dydx,
#>   stata_se, margins_dydx, margins_se, emmeans_dydx, emmeans_se
#>   
#>   It can sometimes be useful to supply a data frame explicitly to the
#>   `newdata` argument in order to be able to group by different columns.

# cross
marginal_means(mod,
  variables = c("cyl", "carb"),
  cross = TRUE)
#> Error: Elements of the `variables` argument were not found as column names in
#>   the data used to fit the model: cyl, carb

# collapsed cross
by <- expand.grid(
  cyl = unique(mtcars$cyl),
  carb = unique(mtcars$carb))
by$by <- ifelse(
  by$cyl == 4,
  paste("Control:", by$carb),
  paste("Treatment:", by$carb))


# Convert numeric variables to categorical before fitting the model
dat <- mtcars
dat$am <- as.logical(dat$am)
dat$carb <- as.factor(dat$carb)
mod <- lm(mpg ~ hp + am + carb, data = dat)

# Compute and summarize marginal means
marginal_means(mod)
#> Error: No logical, factor, or character variable was found in the dataset used
#>   to fit the `model` object. This error is often raised when users convert
#>   variables to factor in the model formula (e.g., `lm(y ~ factor(x)`). If
#>   this is the case, you may consider converting variables in the dataset
#>   before fitting the model.

# Contrast between marginal means (carb2 - carb1), or "is the 1st marginal means equal to the 2nd?"
# see the vignette on "Hypothesis Tests and Custom Contrasts" on the `marginaleffects` website.
lc <- c(-1, 1, 0, 0, 0, 0)
marginal_means(mod, variables = "carb", hypothesis = "b2 = b1")
#> Error: Elements of the `variables` argument were not found as column names in
#>   the data used to fit the model: carb

marginal_means(mod, variables = "carb", hypothesis = lc)
#> Error: Elements of the `variables` argument were not found as column names in
#>   the data used to fit the model: carb

# Multiple custom contrasts
lc <- matrix(c(
    -2, 1, 1, 0, -1, 1,
    -1, 1, 0, 0, 0, 0
    ),
  ncol = 2,
  dimnames = list(NULL, c("A", "B")))
marginal_means(mod, variables = "carb", hypothesis = lc)
#> Error: Elements of the `variables` argument were not found as column names in
#>   the data used to fit the model: carb