These methods provide for follow-up analyses of emmGrid objects:
Contrasts, pairwise comparisons, tests, and confidence intervals. They may
also be used to compute arbitrary linear functions of predictions or EMMs.
contrast(object, ...)# S3 method for emmGrid
contrast(object, method = "eff", interaction = FALSE, by,
offset = NULL, name = "contrast", options = get_emm_option("contrast"),
type, adjust, simple, combine = FALSE, ...)
# S3 method for emmGrid
pairs(x, reverse = FALSE, ...)
# S3 method for emmGrid
coef(object, ...)
An object of class emmGrid
Additional arguments passed to other methods
Character value giving the root name of a contrast method (e.g.
"pairwise" -- see emmc-functions). Alternatively, a named
list of coefficients (for a contrast or linear function) that must
each conform to the number of results in each by group. In a
multi-factor situation, the factor levels are combined and treated like a
single factor.
Character vector or logical value. If this is specified,
method is ignored. See the “Interaction contrasts” section
below for details.
Character names of variable(s) to be used for ``by'' groups. The
contrasts or joint tests will be evaluated separately for each combination
of these variables. If object was created with by groups, those are
used unless overridden. Use by = NULL to use no by groups at all.
Numeric vector of the same length as each by group.
These values are added to their respective linear estimates. (It is ignored
when interaction is specified.)
Character name to use to override the default label for contrasts used in table headings or subsequent contrasts of the returned object.
If non-NULL, a named list of arguments to pass
to update.emmGrid, just after the object is constructed.
Character: prediction type (e.g., "response") -- added to
options
Character: adjustment method (e.g., "bonferroni") --
added to options
Character vector or list: Specify the factor(s) not in
by, or a list thereof. See the section below on simple contrasts.
Logical value that determines what is returned when
simple is a list. See the section on simple contrasts.
An emmGrid object
Logical value - determines whether to use "pairwise" (if TRUE) or "revpairwise" (if FALSE).
contrast and pairs return an object of class
emmGrid. Its grid will correspond to the levels of the contrasts and
any by variables. The exception is that an emm_list
object is returned if simple is a list and complete is
FALSE.
coef returns a data.frame containing the object's grid, along with columns named c.1, c.2, ... containing the contrast coefficients. If
The call pairs(object) is equivalent to
contrast(object, method = "pairwise"); and pairs(object,
reverse = TRUE) is the same as contrast(object, method =
"revpairwise").
When interaction is specified,
interaction contrasts are computed: Contrasts are generated for each factor
separately, one at a time; and these contrasts are applied to the object
(the first time around) or to the previous result (subsequently). (Any
factors specified in by are skipped.) The final result comprises
contrasts of contrasts, or, equivalently, products of contrasts for the
factors involved. Processing is done in the order of appearance in
object@levels. With interaction = TRUE, method (if
specified as character) is used for each contrast. If interaction is
a character vector, the elements specify the respective contrast method(s);
they are recycled as needed.
simple is essentially the complement of by: When
simple is a character vector, by is set to all the factors in
the grid except those in simple. If simple is a list,
each element is used in turn as simple, and assembled in an
"emm_list". To generate all simple main effects, use
simple = "each" (this works unless there actually is a factor named
"each"). Note that a non-missing simple will cause by
to be ignored.
Ordinarily, when simple is a list or "each", the return value
is an emm_list object with each entry in correspondence with
the entries of simple. However, with combine = TRUE, the
elements are all combined into one family of contrasts in a single
emmGrid object using
rbind.emmGrid.. In that case, the adjust argument sets
the adjustment method for the combined set of contrasts.
# NOT RUN {
warp.lm <- lm(breaks ~ wool*tension, data = warpbreaks)
warp.emm <- emmeans(warp.lm, ~ tension | wool)
contrast(warp.emm, "poly") # inherits 'by = "wool"' from warp.emm
pairs(warp.emm) # ditto
contrast(warp.emm, "eff", by = NULL) # contrasts of the 6 factor combs
pairs(warp.emm, simple = "wool") # same as pairs(warp.emm, by = "tension")
# Do all "simple" comparisons, combined into one family
pairs(warp.emm, simple = "each", combine = TRUE)
# }
# NOT RUN {
## Note that the following are NOT the same:
contrast(warp.emm, simple = c("wool", "tension"))
contrast(warp.emm, simple = list("wool", "tension"))
## The first generates contrasts for combinations of wool and tension
## (same as by = NULL)
## The second generates contrasts for wool by tension, and for
## tension by wool, respectively.
# }
# NOT RUN {
# An interaction contrast for tension:wool
tw.emm <- contrast(warp.emm, interaction = c("poly", "consec"), by = NULL)
tw.emm # see the estimates
coef(tw.emm) # see the contrast coefficients
# }
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