Compute estimated marginal means (EMMs) for specified factors or factor combinations in a linear model; and optionally, comparisons or contrasts among them. EMMs are also known as least-squares means.
emmeans(object, specs, by = NULL, fac.reduce = function(coefs) apply(coefs, 2, mean), contr, options = get_emm_option("emmeans"), weights, offset, trend, ..., tran)
An object of class
A character vector specifying the names of predictors to condition on.
A function that combines the rows of a matrix into a single
vector. This implements the “marginal averaging” aspect of EMMs.
The default is the mean of the rows. Typically if it is overridden,
it would be some kind of weighted mean of the rows. If
A character value or
Character value, numeric vector, or numeric matrix specifying
weights to use in averaging predictions. See “Weights” section below.
Numeric vector or scalar. If specified, this adds an offset to the predictions, or overrides any offset in the model or its reference grid. If a vector of length differing from the number of rows in the result, it is subsetted or cyclically recycled.
This is now deprecated. Use
These arguments may also be used in lieu of
Placeholder to prevent it from being included in
Users should also consult the documentation for
because many important options for EMMs are implemented there, via the
specs is a
character vector or one-sided formula,
an object of class
"emmGrid". A number of methods
are provided for further analysis, including
specs is a
list or a
formula having a left-hand
side, the return value is an
emm_list object, which is simply a
Estimated marginal means or EMMs (sometimes called least-squares means) are
predictions from a linear model over a reference grid; or marginal
averages thereof. The
ref_grid function identifies/creates the
reference grid upon which
emmeans is based.
For those who prefer the terms “least-squares means” or
“predicted marginal means”, functions
pmmeans are provided as wrappers. See
specs is a
formula, it should be of the form
~ specs | by,
contr ~ specs, or
contr ~ specs | by. The
formula is parsed and the variables therein are used as the arguments
contr as indicated. The left-hand side is
optional, but if specified it should be the name of a contrast family (e.g.,
pairwise). Operators like
: are needed in the formula to delineate names, but
otherwise are ignored.
In the special case where the mean (or weighted mean) of all the predictions
is desired, specify
~ 1 or
A number of standard contrast families are provided. They can be identified
as functions having names ending in
.emmc – see the documentation
emmc-functions for details – including how to write your
.emmc function for custom contrasts.
weights is a vector, its length must equal
the number of predictions to be averaged to obtain each EMM.
If a matrix, each row of the matrix is used in turn, wrapping back to the
first row as needed. When in doubt about what is being averaged (or how
many), first call
weights = "show.levels".
weights is a string, it should partially match one of the following:
Use an equally weighted average.
Weight in proportion to the frequencies (in the original data) of the factor combinations that are averaged over.
Weight in proportion to each individual factor's marginal frequencies. Thus, the weights for a combination of factors are the outer product of the one-factor margins
Weight according to the frequencies of the cells being averaged.
Give equal weight to all cells with data, and ignore empty cells.
This is a convenience feature for understanding what is being averaged over. Instead of a table of EMMs, this causes the function to return a table showing the levels that are averaged over, in the order that they appear.
Outer weights are like the 'expected' counts in a chi-square test of
independence, and will yield the same results as those obtained by
proportional averaging with one factor at a time. All except
uses the same set of weights for each mean. In a model where the predicted
values are the cell means, cell weights will yield the raw averages of the
data for the factors involved. Using
"flat" is similar to
"cells", except nonempty cells are weighted equally and empty cells
ref_grid, an offset need not be scalar. If not enough values
are supplied, they are cyclically recycled. For a vector of offsets, it is
important to understand that the ordering of results goes with the first
specs varying fastest. If there are any
those vary slower than all the primary ones, but the first
varies the fastest within that hierarchy. See the examples.
Arguments that could go in
options may instead be included in
typically, arguments such as
infer, etc. that in essence
are passed to
summary.emmGrid. Arguments in both places are
overridden by the ones in
There is a danger that
... arguments could partially match those used
update.emmGrid, creating a conflict.
If these occur, usually they can be resolved by providing complete (or at least
longer) argument names; or by isolating non-
ref_grid arguments in
options; or by calling
ref_grid separately and passing the
object. See a not-run example below.
specs is a two-sided formula, or
contr is specified,
there is potential confusion concerning which
apply to the means, and which to the contrasts. When such confusion is possible,
we suggest doing things separately
(a call to
emmeans with no contrasts, followed by a call to
contrast). We do treat
adjust as a special case: it is applied to the
only if there are
no contrasts specified, otherwise it is passed to
warp.lm <- lm(breaks ~ wool * tension, data = warpbreaks) emmeans (warp.lm, ~ wool | tension) # or equivalently emmeans(warp.lm, "wool", by = "tension") # 'adjust' argument ignored in emmeans, passed to contrast part... emmeans (warp.lm, poly ~ tension | wool, adjust = "sidak") ## Not run: # 'adjust' argument NOT ignored ... emmeans (warp.lm, ~ tension | wool, adjust = "sidak") ## End(Not run) ## Not run: ### Offsets: Consider a silly example: emmeans(warp.lm, ~ tension | wool, offset = c(17, 23, 47)) @ grid # note that offsets are recycled so that each level of tension receives # the same offset for each wool. # But using the same offsets with ~ wool | tension will probably not # be what you want because the ordering of combinations is different. ## End(Not run)
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