Package 'ggeffects'

Description

After fitting a model, it is useful generate model-based estimates (expected values, or adjusted predictions) of the response variable for different combinations of predictor values. Such estimates can be used to make inferences about relationships between variables.

The ggeffects package computes marginal means and adjusted predicted values for the response, at the margin of specific values or levels from certain model terms. The package is built around three core functions: predict_response() (understanding results), test_predictions() (testing results for statistically significant differences) and plot() (communicate results).

By default, adjusted predictions or marginal means are by returned on the response scale, which is the easiest and most intuitive scale to interpret the results. There are other options for specific models as well, e.g. with zero-inflation component (see documentation of the type-argument). The result is returned as consistent data frame, which is nicely printed by default. plot() can be used to easily create figures.

The main function to calculate marginal means and adjusted predictions is predict_response(). In previous versions of ggeffects, the functions ggpredict(), ggemmeans(), ggeffect() and ggaverage() were used to calculate marginal means and adjusted predictions. These functions are still available, but predict_response() as a "wrapper" around these functions is the preferred way to do this now.

• ggpredict() calls get_predictions() (which in turn calls stats::predict())

• ggemmeans() calls emmeans::emmeans()

• ggaverage() calls marginaleffects::avg_predictions()

• ggeffect() calls effects::Effect()

Usage

## S3 method for class 'ggeffects'
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  ...,
  stringsAsFactors = FALSE,
  terms_to_colnames = FALSE
)

ggaverage(
  model,
  terms,
  ci_level = 0.95,
  type = "fixed",
  typical = "mean",
  condition = NULL,
  back_transform = TRUE,
  vcov = NULL,
  vcov_args = NULL,
  weights = NULL,
  verbose = TRUE,
  ...
)

ggeffect(
  model,
  terms,
  ci_level = 0.95,
  bias_correction = FALSE,
  verbose = TRUE,
  ...
)

ggemmeans(
  model,
  terms,
  ci_level = 0.95,
  type = "fixed",
  typical = "mean",
  condition = NULL,
  interval = "confidence",
  back_transform = TRUE,
  vcov = NULL,
  vcov_args = NULL,
  bias_correction = FALSE,
  weights = NULL,
  verbose = TRUE,
  ...
)

ggpredict(
  model,
  terms,
  ci_level = 0.95,
  type = "fixed",
  typical = "mean",
  condition = NULL,
  interval = "confidence",
  back_transform = TRUE,
  vcov = NULL,
  vcov_args = NULL,
  bias_correction = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Details

Please see ?predict_response for details and examples.

Value

A data frame (with ggeffects class attribute) with consistent data columns:

• "x": the values of the first term in terms, used as x-position in plots.

• "predicted": the predicted values of the response, used as y-position in plots.

• "std.error": the standard error of the predictions. Note that the standard errors are always on the link-scale, and not back-transformed for non-Gaussian models!

• "conf.low": the lower bound of the confidence interval for the predicted values.

• "conf.high": the upper bound of the confidence interval for the predicted values.

• "group": the grouping level from the second term in terms, used as grouping-aesthetics in plots.

• "facet": the grouping level from the third term in terms, used to indicate facets in plots.

  The estimated marginal means (or predicted values) are always on the response scale!

  For proportional odds logistic regression (see ?MASS::polr) resp. cumulative link models (e.g., see ?ordinal::clm), an additional column "response.level" is returned, which indicates the grouping of predictions based on the level of the model's response.

  Note that for convenience reasons, the columns for the intervals are always named "conf.low" and "conf.high", even though for Bayesian models credible or highest posterior density intervals are returned.

  There is an as.data.frame() method for objects of class ggeffects, which has an terms_to_colnames argument, to use the term names as column names instead of the standardized names "x" etc.

Description

A sample data set from a course about the analysis of factorial designs, by Mattan S. Ben-Shachar. See following link for more information: https://github.com/mattansb/Analysis-of-Factorial-Designs-foR-Psychologists

The data consists of five variables from 120 observations:

• ID: A unique identifier for each participant

• sex: The participant's sex

• time: The time of day the participant was tested (morning, noon, or afternoon)

• coffee: Group indicator, whether participant drank coffee or not ("⁠coffee"⁠ or "control").

• alertness: The participant's alertness score.

Examples

# Attach coffee-data
data(coffee_data)

Description

This function extracts the raw data points (i.e. the data that was used to fit the model) and "averages" (i.e. "collapses") the response variable over the levels of the grouping factor given in collapse_by. Only works with mixed models.

Usage

collapse_by_group(grid, model, collapse_by = NULL, residuals = FALSE)

Arguments

Value

A data frame with raw data points, averaged over the levels of the given grouping factor from the random effects. The group level of the random effect is saved in the column "random".

Examples

library(ggeffects)
data(efc, package = "ggeffects")
efc$e15relat <- as.factor(efc$e15relat)
efc$c161sex <- as.factor(efc$c161sex)
levels(efc$c161sex) <- c("male", "female")
model <- lme4::lmer(neg_c_7 ~ c161sex + (1 | e15relat), data = efc)
me <- predict_response(model, terms = "c161sex")
head(attributes(me)$rawdata)
collapse_by_group(me, model, "e15relat")

Description

An SPSS sample data set, imported with the sjlabelled::read_spss() function. Consists of 28 variables from 908 observations. The data set is part of the EUROFAMCARE project, a cross-national survey on informal caregiving in Europe.

Examples

# Attach EFC-data
data(efc)

# Show structure
str(efc)

# show first rows
head(efc)

Description

A sample data set, used in tests and some examples. Useful for demonstrating count models (with or without zero-inflation component). It consists of nine variables from 250 observations.

Description

A generic print-method for ggeffects-objects.

Usage

## S3 method for class 'ggeffects'
format(
  x,
  variable_labels = FALSE,
  value_labels = FALSE,
  group_name = FALSE,
  row_header_separator = ", ",
  digits = 2,
  collapse_ci = FALSE,
  collapse_tables = FALSE,
  n,
  ...
)

## S3 method for class 'ggcomparisons'
format(x, collapse_ci = FALSE, collapse_p = FALSE, combine_levels = FALSE, ...)

## S3 method for class 'ggeffects'
print(x, group_name = TRUE, digits = 2, verbose = TRUE, ...)

## S3 method for class 'ggeffects'
print_md(x, group_name = TRUE, digits = 2, ...)

## S3 method for class 'ggeffects'
print_html(
  x,
  group_name = TRUE,
  digits = 2,
  theme = NULL,
  engine = c("tt", "gt"),
  ...
)

## S3 method for class 'ggcomparisons'
print(x, collapse_tables = FALSE, ...)

## S3 method for class 'ggcomparisons'
print_html(
  x,
  collapse_ci = FALSE,
  collapse_p = FALSE,
  theme = NULL,
  engine = c("tt", "gt"),
  ...
)

## S3 method for class 'ggcomparisons'
print_md(x, collapse_ci = FALSE, collapse_p = FALSE, theme = NULL, ...)

Arguments

Value

format() return a formatted data frame, print() prints a formatted data frame to the console. print_html() returns a tinytable object by default (unless changed with engine = "gt"), which is printed as HTML, markdown or LaTeX table (depending on the context from which print_html() is called, see tinytable::tt() for details).

Global Options to Customize Tables when Printing

The verbose argument can be used to display or silence messages and warnings. Furthermore, options() can be used to set defaults for the print() and print_html() method. The following options are available, which can simply be run in the console:

• ggeffects_ci_brackets: Define a character vector of length two, indicating the opening and closing parentheses that encompass the confidence intervals values, e.g. options(ggeffects_ci_brackets = c("[", "]")).

• ggeffects_collapse_ci: Logical, if TRUE, the columns with predicted values (or contrasts) and confidence intervals are collapsed into one column, e.g. options(ggeffects_collapse_ci = TRUE).

• ggeffects_collapse_p: Logical, if TRUE, the columns with predicted values (or contrasts) and p-values are collapsed into one column, e.g. options(ggeffects_collapse_p = TRUE). Note that p-values are replaced by asterisk-symbols (stars) or empty strings when ggeffects_collapse_p = TRUE, depending on the significance level.

• ggeffects_collapse_tables: Logical, if TRUE, multiple tables for subgroups are combined into one table. Only works when there is more than one focal term, e.g. options(ggeffects_collapse_tables = TRUE).

• ggeffects_output_format: String, either "text", "markdown" or "html". Defines the default output format from predict_response(). If "html", a formatted HTML table is created and printed to the view pane. "markdown" creates a markdown-formatted table inside Rmarkdown documents, and prints a text-format table to the console when used interactively. If "text" or NULL, a formatted table is printed to the console, e.g. options(ggeffects_output_format = "html").

• ggeffects_html_engine: String, either "tt" or "gt". Defines the default engine to use for printing HTML tables. If "tt", the tinytable package is used, if "gt", the gt package is used, e.g. options(ggeffects_html_engine = "gt").

Use ⁠options(<option_name> = NULL)⁠ to remove the option.

Examples

data(efc, package = "ggeffects")
fit <- lm(barthtot ~ c12hour + e42dep, data = efc)

# default print
predict_response(fit, "e42dep")

# surround CI values with parentheses
print(predict_response(fit, "e42dep"), ci_brackets = c("(", ")"))
# you can also use `options(ggeffects_ci_brackets = c("[", "]"))`
# to set this globally

# collapse CI columns into column with predicted values
print(predict_response(fit, "e42dep"), collapse_ci = TRUE)

# include value labels
print(predict_response(fit, "e42dep"), value_labels = TRUE)

# include variable labels in column headers
print(predict_response(fit, "e42dep"), variable_labels = TRUE)

# include value labels and variable labels
print(predict_response(fit, "e42dep"), variable_labels = TRUE, value_labels = TRUE)

data(iris)
m <- lm(Sepal.Length ~ Species * Petal.Length, data = iris)

# default print with subgroups
predict_response(m, c("Petal.Length", "Species"))

# omit name of grouping variable in subgroup table headers
print(predict_response(m, c("Petal.Length", "Species")), group_name = FALSE)

# collapse tables into one
print(predict_response(m, c("Petal.Length", "Species")), collapse_tables = TRUE, n = 3)

# increase number of digits
print(predict_response(fit, "e42dep"), digits = 5)

Description

get_predictions() is the core function to return adjusted predictions for a model, when calling ggpredict() or predict_response() with margin = "mean_reference" (the default option for margin). Basically, the input contains the model object and a data grid that is typically used for the newdata argument of the predict() method. get_predictions() can be used as S3-method for own classes, to add support for new models in ggeffects and is only relevant for package developers.

There are no S3-class definitions for ggemmeans() or ggaverage(), because these functions simply call methods from the emmeans or marginaleffects packages. Hence, methods should be written for those packages, too, if a model-object should work with ggemmeans() or ggaverage().

Usage

get_predictions(model, ...)

## Default S3 method:
get_predictions(
  model,
  data_grid = NULL,
  terms = NULL,
  ci_level = 0.95,
  type = NULL,
  typical = NULL,
  vcov = NULL,
  vcov_args = NULL,
  condition = NULL,
  interval = "confidence",
  bias_correction = FALSE,
  link_inverse = insight::link_inverse(model),
  model_info = NULL,
  verbose = TRUE,
  ...
)

Arguments

Details

Adding support for ggeffects is quite easy. The user-level function is predict_response(), which either calls ggpredict(), ggemmeans() or ggaverage(). These function, in turn, call predict(), emmeans::emmeans() or marginaleffects::avg_predictions(). Following needs to be done to add support for new model classes:

• emmeans: if your model is supported by emmeans, it is automatically supported by ggemmeans(). Thus, you need to add the corresponding methods to your package so that your model class is supported by **emmeans.

• marginaleffects: similar to emmeans, if your package is supported by the marginaleffects package, it works with ggaverage().

• predict: in order to make your model class work with ggpredict(), you need to add a get_predictions() method. The here documented arguments are all passed from predict_response() to get_predictions(), no matter if they are required to calculate predictions or not. Thus, it is not necessary to process all of those arguments, but they can be used to modulate certain settings when calculating predictions. Note that if your method does not define all mentioned arguments, these are still passed via ... - make sure that further methods in your get_predictions() method still work when they process the .... It is important that the function returns a data frame with a specific structure, namely the data grid and the columns predicted, conf.low, and conf.high. Predictions and intervals should be on the response scale.

A simple example for an own class-implementation for Gaussian-alike models could look like this:

get_predictions.own_class <- function(model, data_grid, ci_level = 0.95, ...) {
  predictions <- predict(
    model,
    newdata = data_grid,
    type = "response",
    se.fit = !is.na(ci_level),
    ...
  )

  # do we have standard errors?
  if (is.na(ci_level)) {
    # copy predictions
    data_grid$predicted <- as.vector(predictions)
  } else {
    # copy predictions
    data_grid$predicted <- predictions$fit

    # calculate CI
    data_grid$conf.low <- predictions$fit - qnorm(0.975) * predictions$se.fit
    data_grid$conf.high <- predictions$fit + qnorm(0.975) * predictions$se.fit

    # optional: copy standard errors
    attr(data_grid, "std.error") <- predictions$se.fit
  }

  data_grid
}

A simple example for an own class-implementation for non-Gaussian-alike models could look like this (note the use of the link-inverse function link_inverse(), which is passed to the link_inverse argument):

get_predictions.own_class <- function(model,
                                      data_grid,
                                      ci_level = 0.95,
                                      link_inverse = insight::link_inverse(model),
                                      ...) {
  predictions <- predict(
    model,
    newdata = data_grid,
    type = "link", # for non-Gaussian, return on link-scale
    se.fit = !is.na(ci_level),
    ...
  )

  # do we have standard errors?
  if (is.na(ci_level)) {
    # copy predictions
    data_grid$predicted <- link_inverse(as.vector(predictions))
  } else {
    # copy predictions, use link-inverse to back-transform
    data_grid$predicted <- link_inverse(predictions$fit)

    # calculate CI
    data_grid$conf.low <- link_inverse(
      predictions$fit - qnorm(0.975) * predictions$se.fit
    )
    data_grid$conf.high <- link_inverse(
      predictions$fit + qnorm(0.975) * predictions$se.fit
    )

    # optional: copy standard errors
    attr(data_grid, "std.error") <- predictions$se.fit
  }

  data_grid
}

Value

A data frame that contains

• the data grid (from the argument data_grid)

• the columns predicted, conf.low, and conf.high

• optionally, the attribute "std.error" with the standard errors.

Note that predictions and confidence intervals should already be transformed to the response scale (e.g., by using insight::link_inverse()). The standard errors are always on the link scale (not transformed).

If values are not available (for example, confidence intervals), set their value to NA.

Description

Get variable and value labels from ggeffects-objects. predict_response() saves information on variable names and value labels as additional attributes in the returned data frame. This is especially helpful for labelled data (see sjlabelled), since these labels can be used to set axis labels and titles.

Usage

get_title(x, case = NULL)

get_x_title(x, case = NULL)

get_y_title(x, case = NULL)

get_legend_title(x, case = NULL)

get_legend_labels(x, case = NULL)

get_x_labels(x, case = NULL)

get_complete_df(x, case = NULL)

Arguments

Value

The titles or labels as character string, or NULL, if variables had no labels; get_complete_df() returns the input list x as single data frame, where the grouping variable indicates the predicted values for each term.

Examples

library(ggeffects)
library(ggplot2)
data(efc, package = "ggeffects")
efc$c172code <- datawizard::to_factor(efc$c172code)
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)

mydf <- predict_response(fit, terms = c("c12hour", "c161sex", "c172code"))

ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
  stat_smooth(method = "lm") +
  facet_wrap(~facet, ncol = 2) +
  labs(
    x = get_x_title(mydf),
    y = get_y_title(mydf),
    colour = get_legend_title(mydf)
  )

# adjusted predictions, a list of data frames (one data frame per term)
eff <- ggeffect(fit)
eff
get_complete_df(eff)

# adjusted predictions for education only, and get x-axis-labels
mydat <- eff[["c172code"]]
ggplot(mydat, aes(x = x, y = predicted, group = group)) +
  stat_summary(fun = sum, geom = "line") +
  scale_x_discrete(labels = get_x_labels(mydat))

Description

This function can be used to install the latest package version of ggeffects, either the development version (from R-universe/GitHub) or the current version from CRAN.

Usage

install_latest(
  source = c("development", "cran"),
  force = FALSE,
  verbose = TRUE
)

Arguments

Value

Invisible NULL.

Examples

# install latest development-version of ggeffects from the
# r-universe repository
install_latest()

Description

Function conduct a spotlight-analysis to create so-called Johnson-Neyman intervals. The plot() method can be used to visualize the results of the Johnson-Neyman test.

Usage

johnson_neyman(x, precision = 500, p_adjust = NULL, ...)

spotlight_analysis(x, precision = 500, p_adjust = NULL, ...)

## S3 method for class 'ggjohnson_neyman'
plot(
  x,
  colors = c("#f44336", "#2196F3"),
  show_association = TRUE,
  show_rug = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Details

The Johnson-Neyman intervals help to understand where slopes are significant in the context of interactions in regression models. Thus, the interval is only useful if the model contains at least one interaction term. The function accepts the results of a call to predict_response(). The first and the last focal term used in the terms argument of predict_response() must be numeric. The function will then test the slopes of the first focal terms against zero, for different moderator values of the last focal term. If only one numeric focal term is given, the function will create contrasts by levels of the categorical focal term. Use plot() to create a plot of the results.

To avoid misleading interpretations of the plot, we speak of "positive" and "negative" associations, respectively, and "no clear" associations (instead of "significant" or "non-significant"). This should prevent the user from considering a non-significant range of values of the moderator as "accepting the null hypothesis".

Value

A data frame including contrasts of the test_predictions() for the given interaction terms; for plot(), returns a Johnson-Neyman plot.

P-value adjustment for multiple comparisons

Note that p-value adjustment for methods supported by p.adjust() (see also p.adjust.methods), each row is considered as one set of comparisons, no matter which test was specified. That is, for instance, when test_predictions() returns eight rows of predictions (when test = NULL), and p_adjust = "bonferroni", the p-values are adjusted in the same way as if we had a test of pairwise comparisons (test = "pairwise") where eight rows of comparisons are returned. For methods "tukey" or "sidak", a rank adjustment is done based on the number of combinations of levels from the focal predictors in terms. Thus, the latter two methods may be useful for certain tests only, in particular pairwise comparisons.

For johnson_neyman(), the only available adjustment methods are "fdr" (or "bh") (Benjamini & Hochberg (1995)) and "esarey" (or "es") (Esarey and Sumner 2017). These usually return similar results. The major difference is that "fdr" can be slightly faster and more stable in edge cases, however, confidence intervals are not updated. Only the p-values are adjusted. "esarey" is slower, but confidence intervals are updated as well.

References

Bauer, D. J., & Curran, P. J. (2005). Probing interactions in fixed and multilevel regression: Inferential and graphical techniques. Multivariate Behavioral Research, 40(3), 373-400. doi: 10.1207/s15327906mbr4003_5

Esarey, J., & Sumner, J. L. (2017). Marginal effects in interaction models: Determining and controlling the false positive rate. Comparative Political Studies, 1–33. Advance online publication. doi: 10.1177/0010414017730080

Johnson, P.O. & Fay, L.C. (1950). The Johnson-Neyman technique, its theory and application. Psychometrika, 15, 349-367. doi: 10.1007/BF02288864

McCabe CJ, Kim DS, King KM. Improving Present Practices in the Visual Display of Interactions. Advances in Methods and Practices in Psychological Science. 2018;1(2):147-165. doi:10.1177/2515245917746792

Spiller, S. A., Fitzsimons, G. J., Lynch, J. G., & McClelland, G. H. (2013). Spotlights, Floodlights, and the Magic Number Zero: Simple Effects Tests in Moderated Regression. Journal of Marketing Research, 50(2), 277–288. doi:10.1509/jmr.12.0420

Examples

## Not run: 
data(efc, package = "ggeffects")
efc$c172code <- as.factor(efc$c172code)
m <- lm(neg_c_7 ~ c12hour * barthtot * c172code, data = efc)

pr <- predict_response(m, c("c12hour", "barthtot"))
johnson_neyman(pr)
plot(johnson_neyman(pr))

pr <- predict_response(m, c("c12hour", "c172code", "barthtot"))
johnson_neyman(pr)
plot(johnson_neyman(pr))

# robust standard errors
if (requireNamespace("sandwich")) {
  johnson_neyman(pr, vcov = sandwich::vcovHC)
}

## End(Not run)

Description

A sample data set, used in tests and examples for survival models. This dataset is originally included in the survival package, but for convenience reasons it is also available in this package.

Description

Create a data frame for the "newdata"-argument that contains all combinations of values from the terms in questions. Similar to expand.grid(). The terms-argument accepts all shortcuts for representative values as in predict_response().

Usage

new_data(model, terms, typical = "mean", condition = NULL, ...)

data_grid(model, terms, typical = "mean", condition = NULL, ...)

Arguments

Value

A data frame containing one row for each combination of values of the supplied variables.

Examples

data(efc, package = "ggeffects")
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
new_data(fit, c("c12hour [meansd]", "c161sex"))

nd <- new_data(fit, c("c12hour [meansd]", "c161sex"))
pr <- predict(fit, type = "response", newdata = nd)
nd$predicted <- pr
nd

# compare to
predict_response(fit, c("c12hour [meansd]", "c161sex"))

Description

plot is a generic plot-method for ggeffects-objects. ggeffects_palette() returns show_palettes()

Usage

## S3 method for class 'ggeffects'
plot(
  x,
  show_ci = TRUE,
  ci_style = c("ribbon", "errorbar", "dash", "dot"),
  show_data = FALSE,
  show_residuals = FALSE,
  show_residuals_line = FALSE,
  data_labels = FALSE,
  limit_range = FALSE,
  collapse_group = FALSE,
  show_legend = TRUE,
  show_title = TRUE,
  show_x_title = TRUE,
  show_y_title = TRUE,
  case = NULL,
  colors = NULL,
  alpha = 0.15,
  dot_size = NULL,
  dot_alpha = 0.35,
  dot_shape = NULL,
  line_size = NULL,
  jitter = NULL,
  dodge = 0.25,
  use_theme = TRUE,
  log_y = FALSE,
  connect_lines = FALSE,
  facets,
  grid,
  one_plot = TRUE,
  n_rows = NULL,
  verbose = TRUE,
  ...
)

theme_ggeffects(base_size = 11, base_family = "")

ggeffects_palette(palette = "metro", n = NULL)

show_palettes()

Arguments

Details

For proportional odds logistic regression (see ?MASS::polr) or cumulative link models in general, plots are automatically facetted by response.level, which indicates the grouping of predictions based on the level of the model's response.

Value

A ggplot2-object.

Partial Residuals

For generalized linear models (glms), residualized scores are computed as inv.link(link(Y) + r) where Y are the predicted values on the response scale, and r are the working residuals.

For (generalized) linear mixed models, the random effect are also partialled out.

Note

Load library(ggplot2) and use theme_set(theme_ggeffects()) to set the ggeffects-theme as default plotting theme. You can then use further plot-modifiers, e.g. from sjPlot, like legend_style() or font_size() without losing the theme-modifications.

There are pre-defined colour palettes in this package. Use show_palettes() to show all available colour palettes as plot, or ggeffects_palette(palette = NULL) to show the color codes.

Examples

library(sjlabelled)
data(efc)
efc$c172code <- as_label(efc$c172code)
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)

dat <- predict_response(fit, terms = "c12hour")
plot(dat)


# facet by group, use pre-defined color palette
dat <- predict_response(fit, terms = c("c12hour", "c172code"))
plot(dat, facet = TRUE, colors = "hero")

# don't use facets, b/w figure, w/o confidence bands
dat <- predict_response(fit, terms = c("c12hour", "c172code"))
plot(dat, colors = "bw", show_ci = FALSE)

# factor at x axis, plot exact data points and error bars
dat <- predict_response(fit, terms = c("c172code", "c161sex"))
plot(dat)

# for three variables, automatic facetting
dat <- predict_response(fit, terms = c("c12hour", "c172code", "c161sex"))
plot(dat)


# show color codes of specific palette
ggeffects_palette("okabe-ito")

# show all color palettes
show_palettes()

Description

This function "pools" (i.e. combines) multiple ggcomparisons objects, returned by test_predictions(), in a similar fashion as mice::pool().

Usage

pool_comparisons(x, ...)

Arguments

Details

Averaging of parameters follows Rubin's rules (Rubin, 1987, p. 76).

Value

A data frame with pooled comparisons or contrasts of predictions.

References

Rubin, D.B. (1987). Multiple Imputation for Nonresponse in Surveys. New York: John Wiley and Sons.

Examples

data("nhanes2", package = "mice")
imp <- mice::mice(nhanes2, printFlag = FALSE)
comparisons <- lapply(1:5, function(i) {
  m <- lm(bmi ~ age + hyp + chl, data = mice::complete(imp, action = i))
  test_predictions(m, "age")
})
pool_comparisons(comparisons)

Description

This function "pools" (i.e. combines) multiple ggeffects objects, in a similar fashion as mice::pool().

Usage

pool_predictions(x, ...)

Arguments

Details

Averaging of parameters follows Rubin's rules (Rubin, 1987, p. 76). Pooling is applied to the predicted values on the scale of the linear predictor, not on the response scale, in order to have accurate pooled estimates and standard errors. The final pooled predicted values are then transformed to the response scale, using insight::link_inverse().

Value

A data frame with pooled predictions.

References

Rubin, D.B. (1987). Multiple Imputation for Nonresponse in Surveys. New York: John Wiley and Sons.

Examples

# example for multiple imputed datasets
data("nhanes2", package = "mice")
imp <- mice::mice(nhanes2, printFlag = FALSE)
predictions <- lapply(1:5, function(i) {
  m <- lm(bmi ~ age + hyp + chl, data = mice::complete(imp, action = i))
  predict_response(m, "age")
})
pool_predictions(predictions)

Description

After fitting a model, it is useful generate model-based estimates (expected values, or adjusted predictions) of the response variable for different combinations of predictor values. Such estimates can be used to make inferences about relationships between variables.

The ggeffects package computes marginal means and adjusted predicted values for the response, at the margin of specific values or levels from certain model terms. The package is built around three core functions: predict_response() (understanding results), test_predictions() (importance of results) and plot() (communicate results).

By default, adjusted predictions or marginal means are returned on the response scale, which is the easiest and most intuitive scale to interpret the results. There are other options for specific models as well, e.g. with zero-inflation component (see documentation of the type-argument). The result is returned as structured data frame, which is nicely printed by default. plot() can be used to easily create figures.

The main function to calculate marginal means and adjusted predictions is predict_response(), which returns adjusted predictions, marginal means or averaged counterfactual predictions depending on value of the margin-argument.

In previous versions of ggeffects, the functions ggpredict(), ggemmeans(), ggeffect() and ggaverage() were used to calculate marginal means and adjusted predictions. These functions are still available, but predict_response() as a "wrapper" around these functions is the preferred way to calculate marginal means and adjusted predictions now.

Usage

predict_response(
  model,
  terms,
  margin = "mean_reference",
  ci_level = 0.95,
  type = "fixed",
  condition = NULL,
  interval = "confidence",
  back_transform = TRUE,
  vcov = NULL,
  vcov_args = NULL,
  weights = NULL,
  bias_correction = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

A data frame (with ggeffects class attribute) with consistent data columns:

• "x": the values of the first term in terms, used as x-position in plots.

• "predicted": the predicted values of the response, used as y-position in plots.

• "std.error": the standard error of the predictions. Note that the standard errors are always on the link-scale, and not back-transformed for non-Gaussian models!

• "conf.low": the lower bound of the confidence interval for the predicted values.

• "conf.high": the upper bound of the confidence interval for the predicted values.

• "group": the grouping level from the second term in terms, used as grouping-aesthetics in plots.

• "facet": the grouping level from the third term in terms, used to indicate facets in plots.

  The estimated marginal means (or predicted values) are always on the response scale!

  For proportional odds logistic regression (see ?MASS::polr) resp. cumulative link models (e.g., see ?ordinal::clm), an additional column "response.level" is returned, which indicates the grouping of predictions based on the level of the model's response.

  Note that for convenience reasons, the columns for the intervals are always named "conf.low" and "conf.high", even though for Bayesian models credible or highest posterior density intervals are returned.

  There is an as.data.frame() method for objects of class ggeffects, which has an terms_to_colnames argument, to use the term names as column names instead of the standardized names "x" etc.

Supported Models

A list of supported models can be found at the package website. Support for models varies by marginalization method (the margin argument), i.e. although predict_response() supports most models, some models are only supported exclusively by one of the four downstream functions (ggpredict(), ggemmeans(), ggeffect() or ggaverage()). This means that not all models work for every margin option of predict_response().

Holding covariates at constant values, or how to marginalize over the non-focal predictors

predict_response() is a wrapper around ggpredict(), ggemmeans() and ggaverage(). Depending on the value of the margin argument, predict_response() calls one of those functions. The margin argument indicates how to marginalize over the non-focal predictors, i.e. those variables that are not specified in terms. Possible values are:

• "mean_reference" and "mean_mode": For "mean_reference", non-focal predictors are set to their mean (numeric variables), reference level (factors), or "most common" value (mode) in case of character vectors. For "mean_mode", non-focal predictors are set to their mean (numeric variables) or mode (factors, or "most common" value in case of character vectors).

  These predictons represent a rather "theoretical" view on your data, which does not necessarily exactly reflect the characteristics of your sample. It helps answer the question, "What is the predicted (or: expected) value of the response at meaningful values or levels of my focal terms for a 'typical' observation in my data?", where 'typical' refers to certain characteristics of the remaining predictors.

• "marginalmeans": non-focal predictors are set to their mean (numeric variables) or averaged over the levels or "values" for factors and character vectors. Averaging over the factor levels of non-focal terms computes a kind of "weighted average" for the values at which these terms are hold constant. Thus, non-focal categorical terms are conditioned on "weighted averages" of their levels. There are different weighting options that can be altered using the weights argument.

  These predictions come closer to the sample, because all possible values and levels of the non-focal predictors are taken into account. It would answer the question, "What is the predicted (or: expected) value of the response at meaningful values or levels of my focal terms for an 'average' observation in my data?". It refers to randomly picking a subject of your sample and the result you get on average.

• "empirical" (or "counterfactual" or "average"): non-focal predictors are averaged over the observations in the sample. The response is predicted for each subject in the data and predicted values are then averaged across all subjects, aggregated/grouped by the focal terms. In particular, averaging is applied to counterfactual predictions (Dickerman and Hernan 2020). There is a more detailed description in this vignette.

  Counterfactual predictions are useful, insofar as the results can also be transferred to other contexts. It answers the question, "What is the predicted (or: expected) value of the response at meaningful values or levels of my focal terms for the 'average' observation in the population?". It does not only refer to the actual data in your sample, but also "what would be if" we had more data, or if we had data from a different population. This is where "counterfactual" refers to.

You can set a default-option for the margin argument via options(), e.g. options(ggeffects_margin = "empirical"), so you don't have to specify your "default" marginalization method each time you call predict_response(). Use options(ggeffects_margin = NULL) to remove that setting.

The condition argument can be used to fix non-focal terms to specific values.

Marginal Means and Adjusted Predictions at Specific Values

Meaningful values of focal terms can be specified via the terms argument. Specifying meaningful or representative values as string pattern is the preferred way in the ggeffects package. However, it is also possible to use a list() for the focal terms if prefer the "classical" R way. terms can also be a data (or reference) grid provided as data frame. All options are described in this vignette.

Indicating levels in square brackets allows for selecting only certain groups or values resp. value ranges. The term name and the start of the levels in brackets must be separated by a whitespace character, e.g. terms = c("age", "education [1,3]"). Numeric ranges, separated with colon, are also allowed: terms = c("education", "age [30:60]"). The stepsize for ranges can be adjusted using by, e.g. terms = "age [30:60 by=5]".

The terms argument also supports the same shortcuts as the values argument in values_at(). So terms = "age [meansd]" would return predictions for the values one standard deviation below the mean age, the mean age and one SD above the mean age. terms = "age [quart2]" would calculate predictions at the value of the lower, median and upper quartile of age.

Furthermore, it is possible to specify a function name. Values for predictions will then be transformed, e.g. terms = "income [exp]". This is useful when model predictors were transformed for fitting the model and should be back-transformed to the original scale for predictions. It is also possible to define own functions (see this vignette).

Instead of a function, it is also possible to define the name of a variable with specific values, e.g. to define a vector v = c(1000, 2000, 3000) and then use terms = "income [v]".

You can take a random sample of any size with sample=n, e.g terms = "income [sample=8]", which will sample eight values from all possible values of the variable income. This option is especially useful for plotting predictions at certain levels of random effects group levels, where the group factor has too many levels to be completely plotted. For more details, see this vignette.

Finally, numeric vectors for which no specific values are given, a "pretty range" is calculated (see pretty_range()), to avoid memory allocation problems for vectors with many unique values. If a numeric vector is specified as second or third term (i.e. if this focal term is used for "stratification"), representative values (see values_at()) are chosen (unless other values are specified), which are typically the mean value, as well as one standard deviation below and above the mean. If all values for a numeric vector should be used to compute predictions, you may use e.g. terms = "age [all]". See also package vignettes.

To create a pretty range that should be smaller or larger than the default range (i.e. if no specific values would be given), use the n tag, e.g. terms="age [n=5]" or terms="age [n=12]". Larger values for n return a larger range of predicted values.

Bayesian Regression Models

predict_response() also works with Stan-models from the rstanarm or brms-packages. The predicted values are the median value of all drawn posterior samples. Standard errors are the median absolute deviation of the posterior samples. The confidence intervals for Stan-models are Bayesian predictive intervals. By default, the predictions are based on rstantools::posterior_epred() and hence have the limitations that the uncertainty of the error term (residual variance) is not taken into account. The recommendation is to use the posterior predictive distribution (rstantools::posterior_predict()), i.e. setting interval = "prediction".

Mixed (multilevel) Models

For mixed models, following options are possible:

• Predictions can be made on the population-level (type = "fixed", the default) or for each level of the grouping variable (unit-level). If unit-level predictions are requested, you need to set ⁠type = "random"`` and specify the grouping variable(s) in the ⁠terms' argument.

• Population-level predictions can be either conditional (predictions for a "typical" group) or marginal (average predictions across all groups). The default in predict_response() calculated conditional predictions. Set margin = "empirical" for marginal predictions.

• Prediction intervals, i.e. when interval = "predictions" also account for the uncertainty in the random effects.

See more details in this vignette.

Zero-Inflated and Zero-Inflated Mixed Models with brms

Models of class brmsfit always condition on the zero-inflation component, if the model has such a component. Hence, there is no type = "zero_inflated" nor type = "zi_random" for brmsfit-models, because predictions are based on draws of the posterior distribution, which already account for the zero-inflation part of the model.

Zero-Inflated and Zero-Inflated Mixed Models with glmmTMB

If model is of class glmmTMB, hurdle, zeroinfl or zerotrunc, and margin is not set to ⁠"empirical⁠, simulations from a multivariate normal distribution (see ?MASS::mvrnorm) are drawn to calculate mu*(1-p). Confidence intervals are then based on quantiles of these results. For type = "zi_random", prediction intervals also take the uncertainty in the random-effect paramters into account (see also Brooks et al. 2017, pp.391-392 for details).

An alternative for models fitted with glmmTMB that take all model uncertainties into account are simulations based on simulate(), which is used when type = "simulate" (see Brooks et al. 2017, pp.392-393 for details).

Finally, if margin = "empirical", the returned predictions are already conditioned on the zero-inflation part (and possible random effects) of the model, thus these are most comparable to the type = "simulate" option. In other words, if all model components should be taken into account for predictions, you should consider using margin = "empirical".

MixMod-models from GLMMadaptive

Predicted values for the fixed effects component (type = "fixed" or type = "zero_inflated") are based on predict(..., type = "mean_subject"), while predicted values for random effects components (type = "random" or type = "zi_random") are calculated with predict(..., type = "subject_specific") (see ?GLMMadaptive::predict.MixMod for details). The latter option requires the response variable to be defined in the newdata-argument of predict(), which will be set to its typical value (see values_at()).

Multinomial Models

polr, clm models, or more generally speaking, models with ordinal or multinominal outcomes, have an additional column response.level, which indicates with which level of the response variable the predicted values are associated.

Averaged model predictions (package MuMIn)

For averaged model predictions, i.e. when the input model is an object of class "averaging" (MuMIn::model.avg()), predictions are made with the full averaged coefficients.

Note

Printing Results

The print() method gives a clean output (especially for predictions by groups), and indicates at which values covariates were held constant. Furthermore, the print() method has several arguments to customize the output. See this vignette for details.

Limitations

The support for some models, for example from package MCMCglmm, is not fully tested and may fail for certain models. If you encounter any errors, please file an issue at Github.

References

• Brooks ME, Kristensen K, Benthem KJ van, Magnusson A, Berg CW, Nielsen A, et al. glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling. The R Journal. 2017;9: 378-400.

• Johnson PC. 2014. Extension of Nakagawa & Schielzeth's R2GLMM to random slopes models. Methods Ecol Evol, 5: 944-946.

• Dickerman BA, Hernan, MA. Counterfactual prediction is not only for causal inference. Eur J Epidemiol 35, 615–617 (2020).

Examples

library(sjlabelled)
data(efc)
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)

predict_response(fit, terms = "c12hour")
predict_response(fit, terms = c("c12hour", "c172code"))
# more compact table layout for printing
out <- predict_response(fit, terms = c("c12hour", "c172code", "c161sex"))
print(out, collapse_table = TRUE)

# specified as formula
predict_response(fit, terms = ~ c12hour + c172code + c161sex)

# only range of 40 to 60 for variable 'c12hour'
predict_response(fit, terms = "c12hour [40:60]")

# terms as named list
predict_response(fit, terms = list(c12hour = 40:60))

# covariate "neg_c_7" is held constant at a value of 11.84 (its mean value).
# To use a different value, use "condition"
predict_response(fit, terms = "c12hour [40:60]", condition = c(neg_c_7 = 20))

# to plot ggeffects-objects, you can use the 'plot()'-function.
# the following examples show how to build your ggplot by hand.


# plot predicted values, remaining covariates held constant
library(ggplot2)
mydf <- predict_response(fit, terms = "c12hour")
ggplot(mydf, aes(x, predicted)) +
  geom_line() +
  geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = 0.1)

# three variables, so we can use facets and groups
mydf <- predict_response(fit, terms = c("c12hour", "c161sex", "c172code"))
ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
  stat_smooth(method = "lm", se = FALSE) +
  facet_wrap(~facet, ncol = 2)

# select specific levels for grouping terms
mydf <- predict_response(fit, terms = c("c12hour", "c172code [1,3]", "c161sex"))
ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
  stat_smooth(method = "lm", se = FALSE) +
  facet_wrap(~facet) +
  labs(
    y = get_y_title(mydf),
    x = get_x_title(mydf),
    colour = get_legend_title(mydf)
  )

# level indication also works for factors with non-numeric levels
# and in combination with numeric levels for other variables
data(efc)
efc$c172code <- sjlabelled::as_label(efc$c172code)
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
predict_response(fit, terms = c(
  "c12hour",
  "c172code [low level of education, high level of education]",
  "c161sex [1]"
))

# when "terms" is a named list
predict_response(fit, terms = list(
  c12hour = seq(0, 170, 30),
  c172code = c("low level of education", "high level of education"),
  c161sex = 1
))

# use categorical value on x-axis, use axis-labels, add error bars
dat <- predict_response(fit, terms = c("c172code", "c161sex"))
ggplot(dat, aes(x, predicted, colour = group)) +
  geom_point(position = position_dodge(0.1)) +
  geom_errorbar(
    aes(ymin = conf.low, ymax = conf.high),
    position = position_dodge(0.1)
  ) +
  scale_x_discrete(breaks = 1:3, labels = get_x_labels(dat))

# 3-way-interaction with 2 continuous variables
data(efc)
# make categorical
efc$c161sex <- as_factor(efc$c161sex)
fit <- lm(neg_c_7 ~ c12hour * barthtot * c161sex, data = efc)
# select only levels 30, 50 and 70 from continuous variable Barthel-Index
dat <- predict_response(fit, terms = c("c12hour", "barthtot [30,50,70]", "c161sex"))
ggplot(dat, aes(x = x, y = predicted, colour = group)) +
  stat_smooth(method = "lm", se = FALSE, fullrange = TRUE) +
  facet_wrap(~facet) +
  labs(
    colour = get_legend_title(dat),
    x = get_x_title(dat),
    y = get_y_title(dat),
    title = get_title(dat)
  )

# or with ggeffects' plot-method
plot(dat, show_ci = FALSE)


# predictions for polynomial terms
data(efc)
fit <- glm(
  tot_sc_e ~ c12hour + e42dep + e17age + I(e17age^2) + I(e17age^3),
  data = efc,
  family = poisson()
)
predict_response(fit, terms = "e17age")

Description

Creates an evenly spaced, pretty sequence of numbers for a range of a vector.

Usage

pretty_range(x, n = NULL, length = NULL)

Arguments

Value

A numeric vector with a range corresponding to the minimum and maximum values of x. If x is missing, a function, pre-programmed with n and length is returned. See examples.

Examples

data(iris)
# pretty range for vectors with decimal points
pretty_range(iris$Petal.Length)

# pretty range for large range, increasing by 50
pretty_range(1:1000)

# increasing by 20
pretty_range(1:1000, n = 7)

# return 10 intervals
pretty_range(1:1000, length = 10)

# same result
pretty_range(1:1000, n = 2.5)

# function factory
range_n_5 <- pretty_range(n = 5)
range_n_5(1:1000)

Description

This function computes partial residuals based on a data grid, where the data grid is usually a data frame from all combinations of factor variables or certain values of numeric vectors. This data grid is usually used as newdata argument in predict(), and can be created with new_data().

Usage

residualize_over_grid(grid, model, ...)

## S3 method for class 'data.frame'
residualize_over_grid(grid, model, predictor_name, ...)

## S3 method for class 'ggeffects'
residualize_over_grid(grid, model, protect_names = TRUE, ...)

Arguments

Value

A data frame with residuals for the focal predictor.

Partial Residuals

For generalized linear models (glms), residualized scores are computed as inv.link(link(Y) + r) where Y are the predicted values on the response scale, and r are the working residuals.

For (generalized) linear mixed models, the random effect are also partialled out.

References

Fox J, Weisberg S. Visualizing Fit and Lack of Fit in Complex Regression Models with Predictor Effect Plots and Partial Residuals. Journal of Statistical Software 2018;87.

Examples

library(ggeffects)
set.seed(1234)
x <- rnorm(200)
z <- rnorm(200)
# quadratic relationship
y <- 2 * x + x^2 + 4 * z + rnorm(200)

d <- data.frame(x, y, z)
model <- lm(y ~ x + z, data = d)

pr <- predict_response(model, c("x [all]", "z"))
head(residualize_over_grid(pr, model))

Description

Function to test differences of adjusted predictions for statistical significance. This is usually called contrasts or (pairwise) comparisons, or "marginal effects". hypothesis_test() is an alias.

Usage

test_predictions(object, ...)

hypothesis_test(object, ...)

## Default S3 method:
test_predictions(
  object,
  terms = NULL,
  by = NULL,
  test = "pairwise",
  test_args = NULL,
  equivalence = NULL,
  scale = "response",
  p_adjust = NULL,
  df = NULL,
  ci_level = 0.95,
  collapse_levels = FALSE,
  margin = "mean_reference",
  condition = NULL,
  engine = "marginaleffects",
  verbose = TRUE,
  ...
)

## S3 method for class 'ggeffects'
test_predictions(
  object,
  by = NULL,
  test = "pairwise",
  equivalence = NULL,
  scale = "response",
  p_adjust = NULL,
  df = NULL,
  collapse_levels = FALSE,
  engine = "marginaleffects",
  verbose = TRUE,
  ...
)

Arguments

Value

A data frame containing predictions (e.g. for test = NULL), contrasts or pairwise comparisons of adjusted predictions or estimated marginal means.

Introduction into contrasts and pairwise comparisons

There are many ways to test contrasts or pairwise comparisons. A detailed introduction with many (visual) examples is shown in this vignette.

Simple workflow for pairwise comparisons

A simple workflow includes calculating adjusted predictions and passing the results directly to test_predictions(), e.g.:

# 1. fit your model
model <- lm(mpg ~ hp + wt + am, data = mtcars)
# 2. calculate adjusted predictions
pr <- predict_response(model, "am")
pr
# 3. test pairwise comparisons
test_predictions(pr)

See also this vignette.

Packages used as back-end to calculate contrasts and pairwise comparisons

The test argument is used to define which kind of contrast or comparison should be calculated. The default is to use the marginaleffects package. Here are some technical details about the packages used as back-end. When test is...

• "pairwise" (default), pairwise comparisons are based on the marginaleffects package.

• "trend" or "slope" also uses the marginaleffects package.

• "contrast" uses the emmeans package, i.e. emmeans::contrast(method = "eff") is called.

• "exclude" relies on the emmeans package, i.e. emmeans::contrast(method = "del.eff") is called.

• "polynomial" relies on the emmeans package, i.e. emmeans::contrast(method = "poly") is called.

• "interaction" uses the emmeans package, i.e. emmeans::contrast(interaction = ...) is called.

• "consecutive" also relies on the emmeans package, i.e. emmeans::contrast(method = "consec") is called.

• a character string with a custom hypothesis, the marginaleffects package is used.

• a data frame with custom contrasts, emmeans is used again.

• for formulas, the marginaleffects package is used.

• NULL calls functions from the marginaleffects package with hypothesis = NULL.

• If all focal terms are only present as random effects in a mixed model, or if predicted probabilities for the zero-inflation component of a model should be tested, functions from the ggeffects package are used. There is an example for pairwise comparisons of random effects in this vignette.

P-value adjustment for multiple comparisons

Note that p-value adjustment for methods supported by p.adjust() (see also p.adjust.methods), each row is considered as one set of comparisons, no matter which test was specified. That is, for instance, when test_predictions() returns eight rows of predictions (when test = NULL), and p_adjust = "bonferroni", the p-values are adjusted in the same way as if we had a test of pairwise comparisons (test = "pairwise") where eight rows of comparisons are returned. For methods "tukey" or "sidak", a rank adjustment is done based on the number of combinations of levels from the focal predictors in terms. Thus, the latter two methods may be useful for certain tests only, in particular pairwise comparisons.

For johnson_neyman(), the only available adjustment methods are "fdr" (or "bh") (Benjamini & Hochberg (1995)) and "esarey" (or "es") (Esarey and Sumner 2017). These usually return similar results. The major difference is that "fdr" can be slightly faster and more stable in edge cases, however, confidence intervals are not updated. Only the p-values are adjusted. "esarey" is slower, but confidence intervals are updated as well.

Global options to choose package for calculating comparisons

ggeffects_test_engine can be used as option to either use the marginaleffects package for computing contrasts and comparisons (default), or the emmeans package (e.g. options(ggeffects_test_engine = "emmeans")). The latter is useful when the marginaleffects package is not available, or when the emmeans package is preferred. You can also provide the engine directly, e.g. test_predictions(..., engine = "emmeans"). Note that using emmeans as backend is currently not as feature rich as the default (marginaleffects).

If engine = "emmeans", the test argument can also be "interaction" to calculate interaction contrasts (difference-in-difference contrasts), "consecutive" to calculate contrasts between consecutive levels of a predictor, or a data frame with custom contrasts. If test is one of the latter options, and engine is not specified, the engine is automatically set to "emmeans". Additionally, the test_args argument can be used to specify further options for those contrasts. See 'Examples' and documentation of test_args.

If the marginaleffects package is not installed, the emmeans package is used automatically. If this package is not installed as well, engine = "ggeffects" is used.

Global Options to Customize Tables when Printing

The verbose argument can be used to display or silence messages and warnings. Furthermore, options() can be used to set defaults for the print() and print_html() method. The following options are available, which can simply be run in the console:

• ggeffects_ci_brackets: Define a character vector of length two, indicating the opening and closing parentheses that encompass the confidence intervals values, e.g. options(ggeffects_ci_brackets = c("[", "]")).

• ggeffects_collapse_ci: Logical, if TRUE, the columns with predicted values (or contrasts) and confidence intervals are collapsed into one column, e.g. options(ggeffects_collapse_ci = TRUE).

• ggeffects_collapse_p: Logical, if TRUE, the columns with predicted values (or contrasts) and p-values are collapsed into one column, e.g. options(ggeffects_collapse_p = TRUE). Note that p-values are replaced by asterisk-symbols (stars) or empty strings when ggeffects_collapse_p = TRUE, depending on the significance level.

• ggeffects_collapse_tables: Logical, if TRUE, multiple tables for subgroups are combined into one table. Only works when there is more than one focal term, e.g. options(ggeffects_collapse_tables = TRUE).

• ggeffects_output_format: String, either "text", "markdown" or "html". Defines the default output format from predict_response(). If "html", a formatted HTML table is created and printed to the view pane. "markdown" creates a markdown-formatted table inside Rmarkdown documents, and prints a text-format table to the console when used interactively. If "text" or NULL, a formatted table is printed to the console, e.g. options(ggeffects_output_format = "html").

• ggeffects_html_engine: String, either "tt" or "gt". Defines the default engine to use for printing HTML tables. If "tt", the tinytable package is used, if "gt", the gt package is used, e.g. options(ggeffects_html_engine = "gt").

Use ⁠options(<option_name> = NULL)⁠ to remove the option.

References

Esarey, J., & Sumner, J. L. (2017). Marginal effects in interaction models: Determining and controlling the false positive rate. Comparative Political Studies, 1–33. Advance online publication. doi: 10.1177/0010414017730080

See Also

There is also an equivalence_test() method in the parameters package (parameters::equivalence_test.lm()), which can be used to test contrasts or comparisons for practical equivalence. This method also has a plot() method, hence it is possible to do something like:

library(parameters)
predict_response(model, focal_terms) |>
  equivalence_test() |>
  plot()

Examples

data(efc)
efc$c172code <- as.factor(efc$c172code)
efc$c161sex <- as.factor(efc$c161sex)
levels(efc$c161sex) <- c("male", "female")
m <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)

# direct computation of comparisons
test_predictions(m, "c172code")

# passing a `ggeffects` object
pred <- predict_response(m, "c172code")
test_predictions(pred)

# test for slope
test_predictions(m, "c12hour")

# interaction - contrasts by groups
m <- lm(barthtot ~ c12hour + c161sex * c172code + neg_c_7, data = efc)
test_predictions(m, c("c161sex", "c172code"), test = NULL)

# interaction - pairwise comparisons by groups
test_predictions(m, c("c161sex", "c172code"))

# equivalence testing
test_predictions(m, c("c161sex", "c172code"), equivalence = c(-2.96, 2.96))

# equivalence testing, using the parameters package
pr <- predict_response(m, c("c161sex", "c172code"))
parameters::equivalence_test(pr)

# interaction - collapse unique levels
test_predictions(m, c("c161sex", "c172code"), collapse_levels = TRUE)

# p-value adjustment
test_predictions(m, c("c161sex", "c172code"), p_adjust = "tukey")

# not all comparisons, only by specific group levels
test_predictions(m, "c172code", by = "c161sex")

# specific comparisons
test_predictions(m, c("c161sex", "c172code"), test = "b2 = b1")

# interaction - slope by groups
m <- lm(barthtot ~ c12hour + neg_c_7 * c172code + c161sex, data = efc)
test_predictions(m, c("neg_c_7", "c172code"))

# Interaction and consecutive contrasts -----------------
# -------------------------------------------------------
data(coffee_data, package = "ggeffects")
m <- lm(alertness ~ time * coffee + sex, data = coffee_data)

# consecutive contrasts
test_predictions(m, "time", by = "coffee", test = "consecutive")

# same as (using formula):
pr <- predict_response(m, c("time", "coffee"))
test_predictions(pr, test = difference ~ sequential | coffee)

# interaction contrasts - difference-in-difference comparisons
pr <- predict_response(m, c("time", "coffee"), margin = "marginalmeans")
test_predictions(pr, test = "interaction")

# Ratio contrasts ---------------------------------------
# -------------------------------------------------------
test_predictions(test = ratio ~ reference | coffee)

# Custom contrasts --------------------------------------
# -------------------------------------------------------
wakeup_time <- data.frame(
  "wakeup vs later" = c(-2, 1, 1) / 2, # make sure each "side" sums to (+/-)1!
  "start vs end of day" = c(-1, 0, 1)
)
test_predictions(m, "time", by = "coffee", test = wakeup_time)

# Example: marginal effects -----------------------------
# -------------------------------------------------------
data(iris)
m <- lm(Petal.Width ~ Petal.Length + Species, data = iris)

# we now want the marginal effects for "Species". We can calculate
# the marginal effect using the "marginaleffects" package
marginaleffects::avg_slopes(m, variables = "Species")

# finally, test_predictions() returns the same. while the previous results
# report the marginal effect compared to the reference level "setosa",
# test_predictions() returns the marginal effects for all pairwise comparisons
test_predictions(m, "Species")

Description

This function calculates representative values of a vector, like minimum/maximum values or lower, median and upper quartile etc., which can be used for numeric vectors to plot adjusted predictions at these representative values.

Usage

values_at(x, values = "meansd")

representative_values(x, values = "meansd")

Arguments

Value

A numeric vector, representing the required values from x, like minimum/maximum value or mean and +/- 1 SD. If x is missing, a function, pre-programmed with n and length is returned. See examples.

Examples

data(efc)
values_at(efc$c12hour)
values_at(efc$c12hour, "quartiles2")

mean_sd <- values_at(values = "meansd")
mean_sd(efc$c12hour)

Description

Returns the variance-covariance matrix for the predicted values from object.

Usage

## S3 method for class 'ggeffects'
vcov(object, vcov = NULL, vcov_args = NULL, verbose = TRUE, ...)

Arguments

Details

The returned matrix has as many rows (and columns) as possible combinations of predicted values from the predict_response() call. For example, if there are two variables in the terms-argument of predict_response() with 3 and 4 levels each, there will be 3*4 combinations of predicted values, so the returned matrix has a 12x12 dimension. In short, nrow(object) is always equal to nrow(vcov(object)). See also 'Examples'.

Value

The variance-covariance matrix for the predicted values from object.

Examples

data(efc)
model <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
result <- predict_response(model, c("c12hour [meansd]", "c161sex"))

vcov(result)

# compare standard errors
sqrt(diag(vcov(result)))
as.data.frame(result)

# only two predicted values, no further terms
# vcov() returns a 2x2 matrix
result <- predict_response(model, "c161sex")
vcov(result)

# 2 levels for c161sex multiplied by 3 levels for c172code
# result in 6 combinations of predicted values
# thus vcov() returns a 6x6 matrix
result <- predict_response(model, c("c161sex", "c172code"))
vcov(result)