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Interaction-style plots for estimated marginal means

Source: R/emmip.R
emmip.Rd

Creates an interaction plot of EMMs based on a fitted model and a simple formula specification.

Usage

emmip(object, formula, ...)

# Default S3 method
emmip(object, formula, type, CIs = FALSE, PIs = FALSE,
  style, engine = get_emm_option("graphics.engine"), plotit = TRUE,
  nesting.order = FALSE, ...)

emmip_ggplot(emms, style = "factor", dodge = 0.2, xlab = labs$xlab,
  ylab = labs$ylab, tlab = labs$tlab, facetlab = "label_context", scale,
  dotarg = list(shape = "circle"), linearg = list(linetype = "solid"),
  CIarg = list(alpha = 0.4), PIarg = list(alpha = 0.25), ...)

emmip_lattice(emms, style = "factor", xlab = labs$xlab, ylab = labs$ylab,
  tlab = labs$tlab, pch = c(1, 2, 6, 7, 9, 10, 15:20), lty = 1,
  col = NULL, ...)

Arguments

object

An object of class emmGrid, or a fitted model of a class supported by the emmeans package

formula

Formula of the form trace.factors ~ x.factors | by.factors. The EMMs are plotted against x.factor for each level of trace.factors. by.factors is optional, but if present, it determines separate panels. Each element of this formula may be a single factor in the model, or a combination of factors using the * operator.

...

Additional arguments passed to emmeans (when object is not already an emmGrid object), predict.emmGrid, emmip_ggplot, or emmip_lattice.

type

As in predict.emmGrid, this determines whether we want to inverse-transform the predictions (type = "response") or not (any other choice). The default is "link", unless the "predict.type" option is in force; see emm_options. In addition, the user may specify type = "scale" to create a transformed scale for the vertical axis based on object's response transformation or link function.

CIs

Logical value. If TRUE, confidence intervals (or HPD intervals for Bayesian models) are added to the plot (works only with engine = "ggplot").

PIs

Logical value. If TRUE, prediction intervals are added to the plot (works only with engine = "ggplot"). This is allowed only if the underlying model family is "gaussian". If both CIs and PIs are TRUE, the prediction intervals will be somewhat longer, lighter, and thinner than the confidence intervals. Additional parameters to predict.emmGrid (e.g., sigma) may be passed via .... For Bayesian models, PIs require frequentist = TRUE and a value for sigma.

style

Optional character value. This has an effect only when the horizontal variable is a single numeric variable. If style is unspecified or "numeric", the horizontal scale will be numeric and curves are plotted using lines (and no symbols). With style = "factor", the horizontal variable is treated as the levels of a factor (equally spaced along the horizontal scale), and curves are plotted using lines and symbols. When the horizontal variable is character or factor, or a combination of more than one predictor, "factor" style is always used.

engine

Character value matching "ggplot" (default), "lattice", or "none". The graphics engine to be used to produce the plot. These require, respectively, the ggplot2 or lattice package to be installed. Specifying "none" is equivalent to setting plotit = FALSE.

plotit

Logical value. If TRUE, a graphical object is returned; if FALSE, a data.frame is returned containing all the values used to construct the plot.

nesting.order

Logical value. If TRUE, factors that are nested are presented in order according to their nesting factors, even if those nesting factors are not present in formula. If FALSE, only the variables in formula are used to order the variables.

emms

A data.frame created by calling emmip with plotit = FALSE. Certain variables and attributes are expected to exist in this data frame; see the section detailing the rendering functions.

dodge

Numerical amount passed to ggplot2::position_dodge by which points and intervals are offset so they do not collide.

xlab, ylab, tlab

Character labels for the horizontal axis, vertical axis, and traces (the different curves), respectively. The emmip function generates these automatically and provides therm via the labs attribute, but the user may override these if desired.

facetlab

Labeller for facets (when by variables are in play). Use "label_value" to show just the factor levels, or "label_both" to show both the factor names and factor levels. The default of "label_context" decides which based on how many by factors there are. See the documentation for ggplot2::label_context.

scale

If not missing, an object of class scales::trans specifying a (usually) nonlinear scaling for the vertical axis. For example, scales = scales::log_trans() specifies a logarithmic scale. For fine-tuning purposes, additional arguments to ggplot2::scale_y_continuous may be included in ... .

dotarg

list of arguments passed to geom_point to customize appearance of points. If this includes shape and it is of length greater than 1, it is interpreted as a shape palette instead.

linearg

list of arguments passed to geom_line to customize appearance of lines. If this includes linetype and it is of length greater than 1, it is interpreted as a linetype.

CIarg, PIarg

lists of arguments passed to geom_linerange to customize appearance of intervals. (Note: the linetype aesthetic defaults to "solid" under the hood)

pch

(Lattice only) The plotting characters to use for each group (i.e., levels of trace.factors). They are recycled as needed.

lty

(Lattice only) The line types to use for each group. Recycled as needed.

col

With emmip_ggplot, this adds color = col (not colour) to all of the *arg lists. This is intended for setting a common color for everything, such as a black-and-white plot. With emmip_lattice, col specifies the colors to use for each group, recycled as needed. If not specified, the default trellis colors are used.

Value

If plotit = FALSE, a data.frame (actually, a summary_emm object) with the table of EMMs that would be plotted. The variables plotted are named xvar and yvar, and the trace factor is named tvar. This data frame has an added "labs" attribute containing the labels xlab, ylab, and tlab for these respective variables. The confidence limits are also included, renamed LCL and UCL.

If plotit = TRUE, the function returns an object of class "ggplot" or a "trellis", depending on engine.

Note

Conceptually, this function is equivalent to interaction.plot where the summarization function is thought to return the EMMs.

Details

If object is a fitted model, emmeans is called with an appropriate specification to obtain estimated marginal means for each combination of the factors present in formula (in addition, any arguments in ... that match at, trend, cov.reduce, or fac.reduce are passed to emmeans). Otherwise, if object is an emmGrid object, its first element is used, and it must contain one estimate for each combination of the factors present in formula.

Rendering functions

The functions emmip_ggplot and emmip_lattice are called when plotit == TRUE to render the plots; but they may also be called later on an object saved via plotit = FALSE (or engine = "none"). The functions require that emms contains variables xvar, yvar, and tvar, and attributes "labs" and "vars". Confidence intervals are plotted if variables LCL and UCL exist; and prediction intervals are plotted if LPL and UPL exist. Finally, it must contain the variables named in attr(emms, "vars").

In emmip_ggplot, colors, linetypes, and shapes are all assigned to groups (according to tvar) unless overridden. So, for example, one may have different symbols for each group by simply specifying dotarg = list().

See also

emmeans, interaction.plot.

Examples

#--- Three-factor example
noise.lm = lm(noise ~ size * type * side, data = auto.noise)

# Separate interaction plots of size by type, for each side
emmip(noise.lm, type ~ size | side)


# One interaction plot, using combinations of size and side as the x factor
# ... with added confidence intervals and some formatting changes
emmip(noise.lm, type ~ side * size, CIs = TRUE,
    CIarg = list(linewidth = 1.5, alpha = 1, color = "orange"),
    dotarg = list(size = 2, shape = "square", color = "black"))

    
# Same using legacy theme
with_emm_options(gg.theme = 1,
    emmip(noise.lm, type ~ side * size, CIs = TRUE,
        CIarg = list(linewidth = 1.5, alpha = 1, color = "orange"),
        dotarg = list(size = 2, shape = "square", color = "black")))


# Create a black-and-white version of above with different linetypes
# (Let the linetypes and symbols default to the palette)
emmip(noise.lm, type ~ side * size, CIs = TRUE, col = "black",
      linearg = list(), dotarg = list(size = 2), CIarg = list(alpha = 1)) +
    ggplot2::theme_bw()


# One interaction plot using combinations of type and side as the trace factor
emmip(noise.lm, type * side ~ size)


# Individual traces in panels
emmip(noise.lm, ~ size | type * side)


# Example for the 'style' argument
fib.lm = lm(strength ~ machine * sqrt(diameter), data = fiber)
fib.rg = ref_grid(fib.lm, at = list(diameter = c(12, 14, 15, 25, 36)))
emmip(fib.rg, machine ~ diameter)   # curves (because diameter is numeric)

emmip(fib.rg, machine ~ diameter, style = "factor")  # points and lines


# For an example using extra ggplot2 code, see 'vignette("messy-data")',
# in the section on nested models.

### Options with transformations or link functions
neuralgia.glm <- glm(Pain ~ Treatment * Sex + Age, family = binomial(), 
                     data = neuralgia) 

# On link scale:
emmip(neuralgia.glm, Treatment ~ Sex)


# On response scale:
emmip(neuralgia.glm, Treatment ~ Sex, type = "response")


# With transformed axis scale and custom scale divisions
emmip(neuralgia.glm, Treatment ~ Sex, type = "scale",
    breaks = seq(0.10, 0.90, by = 0.10))