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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, scale = NULL, name = "contrast",
options = get_emm_option("contrast"), type, adjust, simple,
combine = FALSE, ratios = TRUE, parens, ...)
# 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 function
of the same form, or 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, logical value, or list. 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 vectors of the same length as each by group.
The scale values, if supplied, multiply their respective linear estimates, and
any offset values are added. Scalar values are also allowed.
(These arguments are 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.
Logical value determining how log and logit transforms are
handled. These transformations are exceptional cases in that there is a
valid way to back-transform contrasts: differences of logs are logs of
ratios, and differences of logits are odds ratios. If ratios = TRUE
and summarized with type = "response", contrast results are
back-transformed to ratios whenever we have true contrasts (coefficients
sum to zero). For other transformations, there is no natural way to
back-transform contrasts, so even when summarized with type = "response",
contrasts are computed and displayed on the linear-predictor scale. Similarly,
if ratios = FALSE, log and logit transforms are treated in the same way as
any other transformation.
character or NULL. If a character value, the labels for levels
being contrasted are parenthesized if they match the regular expression in
parens[1] (via grep). The default is emm_option("parens").
Optionally, parens may contain second and third elements specifying
what to use for left and right parentheses (default "(" and ")").
Specify parens = NULL or parens = "a^" (which won't match anything)
to disable all parenthesization.
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. Specifically 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. Any named elements of interaction
are assigned to contrast methods; others are assigned in order of
appearance in object@levels. The contrast factors in the resulting
emmGrid object are ordered the same as in interaction.
interaction may be a character vector or list of valid contrast
methods (as documented for the method argument). If the vector or
list is shorter than the number needed, it is recycled. Alternatively, if
the user specifies contrast = TRUE, the contrast specified in
method is used for all factors involved.
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(tension = "poly", wool = "consec"),
by = NULL)
tw.emm # see the estimates
coef(tw.emm) # see the contrast coefficients
# Use of scale and offset
# an unusual use of the famous stack-loss data...
mod <- lm(Water.Temp ~ poly(stack.loss, degree = 2), data = stackloss)
(emm <- emmeans(mod, "stack.loss", at = list(stack.loss = 10 * (1:4))))
# Convert results from Celsius to Fahrenheit:
confint(contrast(emm, "identity", scale = 9/5, offset = 32))
# }
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