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)