contrast: Contrasts and linear functions of EMMs

Description Usage Arguments Value Pairs method Interaction contrasts Simple contrasts Note Examples

View source: R/contrast.R

Description

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.

Usage

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contrast(object, ...)

## S3 method for class '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 class 'emmGrid'
pairs(x, reverse = FALSE, ...)

## S3 method for class 'emmGrid'
coef(object, ...)

Arguments

object

An object of class emmGrid

...

Additional arguments passed to other methods

method

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.

interaction

Character vector, logical value, or list. If this is specified, method is ignored. See the “Interaction contrasts” section below for details.

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 object was created with by groups, those are used unless overridden. Use by = NULL to use no by groups at all.

offset, scale

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.)

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-NULL, a named list of arguments to pass to update.emmGrid, just after the object is constructed.

type

Character: prediction type (e.g., "response") – added to options

adjust

Character: adjustment method (e.g., "bonferroni") – added to options

simple

Character vector or list: Specify the factor(s) not in by, or a list thereof. See the section below on simple contrasts.

combine

Logical value that determines what is returned when simple is a list. See the section on simple contrasts.

ratios

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.

parens

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.

x

An emmGrid object

reverse

Logical value - determines whether to use "pairwise" (if TRUE) or "revpairwise" (if FALSE).

Value

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

Pairs method

The call pairs(object) is equivalent to contrast(object, method = "pairwise"); and pairs(object, reverse = TRUE) is the same as contrast(object, method = "revpairwise").

Interaction contrasts

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 contrasts

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.

Note

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.

Examples

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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(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))

emmeans documentation built on Oct. 25, 2020, 9:06 a.m.