| contrast {lsmeans} | R Documentation |
ref.grid and lsmobj objects
These methods provide for analyses of ref.grid objects, or follow-up analyses of lsmobj objects: Contrasts, pairwise comparisons, tests, and confidence intervals.
## S3 method for class 'ref.grid'
contrast(object, method = "eff", interaction = FALSE,
by, offset = NULL, name = "contrast",
options = getOption("lsmeans")$contrast, adjust, ...)
## S3 method for class 'lsm.list'
contrast(object, ..., which = 1)
## S3 method for class 'ref.grid'
test(object, null = 0, joint = FALSE,
verbose = FALSE, rows, by, ...)
## S3 method for class 'ref.grid'
confint(object, parm, level = 0.95, ...)
## S3 method for class 'ref.grid'
pairs(x, reverse = FALSE, ...)
## S3 method for class 'ref.grid'
coef(object, ...)
object, x |
An object of class |
method |
Character value giving the root name of a contrast method (e.g. ls("package:lsmeans", pat=".lsmc") You may define your own |
interaction |
Character vector or logical value. In multi-factor situations with |
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 |
Name to use to label the contrasts in table headings
or subsequent contrasts of the returned object. This argument is ignored
when |
options |
If non- |
adjust |
Method to use for adjusting P values. This is passed to |
joint |
Logical value. If |
rows |
Integer values. The rows of L to be tested in the joint test. If missing, all rows of L are used. If not missing, |
null |
Numeric value specifying the null value(s) being tested against. It may be either a single value, in which case it is used as the null value for all linear functions under test; or a numeric vector of length equal to the number of linear functions. |
parm |
This is ignored, but it is a required argument of the generic |
verbose |
Logical value. If |
level |
Numeric value of the desired confidence level. |
which |
When |
reverse |
Logical value determining whether |
... |
Additional arguments passed to |
Though contrast is ordinarily used to create true contrasts (whose coefficients sum to zero), it may be used to estimate any linear function of the LS means; and offset expands this capability further by allowing additive constants.
pairs is equivalent to contrast with method = "pairwise".
confint and test (when JOINT==FALSE) are equivalent to calling summary with infer=c(TRUE,FALSE) and infer=c(FALSE,TRUE), respectively.
When using test to do a joint test of L beta = null, an error is thrown if any row of L is non-estimable. It is permissible for the rows of L to be linearly dependent as long as null == 0; a reduced set of contrasts is tested. Linear dependence and nonzero null cause an error.
contrast and pairs return an object of class "lsmobj", which is an extension of "ref.grid". Consequently, they may be used as arguments to other "lsmobj" or "ref.grid" methods. The user may, for example, compute contrasts of contrasts, or re-summarize a set of confidence intervals with a different by grouping or confidence level.
The “grid” for the returned value is simply the set of variables that identify the results. For example, contrast's return value is a reference grid for one factor named contrast.
confint and test (when Joint==FALSE) return an object of class summary.ref.grid. When JOINT==TRUE, test returns a "summary.ref.grid" object (extends "data.frame") with the test statistic, degrees of freedom, and P value for each by group.
When object is the result of a call to contrast or pairs, the coef method returns adata.frame. The initial columns are the factor combinations that were contrasted (i.e. the grid for the object originally specified in the call to contrast), and the remaining columns (named c.1, c.2, ...) contain the contrast coefficients that were applied to the corresponding predictions. If object was not produced via contrast, NULL is returned, along with a message.
Russell V. Lenth
Additional "lsmobj" methods having their own help pages are cld and glht. Also, the summary and other methods for "ref.grid" objects also work for "lsmobj" objects.
require(lsmeans)
warp.lm <- lm(breaks ~ wool*tension, data = warpbreaks)
warp.lsm <- lsmeans(warp.lm, ~ tension | wool)
# Polynomial contrasts of tension, by wool
(warp.pl <- contrast(warp.lsm, "poly", name = "order"))
# Same results with a different adjustment
summary(warp.pl, adjust = "fdr")
# Jointly test the tension effects for each wool
test(warp.pl, joint = TRUE, by = "wool")
# Compare the two contrasts for each order
contrast(warp.pl, "revpairwise", by = "order")
# User-provided contrasts, ignoring the previous by grouping
contrast(warp.lsm,
list(c1=c(1,0,0,-1,0,0), c2=c(1,1,1,-1,-1,-1)/3),
by = NULL)
# Compare consecutive tension*wool comb's as treatment with 6 levels
contrast(warp.lsm, "consec", by = NULL)
# Interaction contrasts (comparisons of linear and quadratic contrasts)
(int.con <- contrast(warp.lsm, interaction = c("poly", "consec"), by = NULL))
# See the contrast coefficients used by the previous call
coef(int.con)