contrast {emmeans} | R Documentation |
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 class '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 class 'emmGrid' pairs(x, reverse = FALSE, ...) ## S3 method for class 'emmGrid' coef(object, ...)
object |
An object of class |
... |
Additional arguments passed to other methods |
method |
Character value giving the root name of a contrast method (e.g.
|
interaction |
Character vector or logical value. If this is specified,
|
by |
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 |
offset |
Numeric vector of the same length as each |
name |
Character name to use to override the default label for contrasts used in table headings or subsequent contrasts of the returned object. |
options |
If non- |
type |
Character: prediction type (e.g., |
adjust |
Character: adjustment method (e.g., |
simple |
Character vector or list: Specify the factor(s) not in
|
combine |
Logical value that determines what is returned when
|
x |
An |
reverse |
Logical value - determines whether to use |
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.
When object
has a nesting structure (this can be seen via
str(object)
), then any grouping factors involved are forced into
service as by
variables, and the contrasts are thus computed
separately in each nest. This in turn may lead to an irregular grid in the
returned emmGrid
object, which may not be valid for subsequent
emmeans
calls.
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. ## End(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