pairwise.lsmc {lsmeans} | R Documentation |
These functions return standard sets of contrast coefficients.
The name of any of these functions (with the .lsmc
omitted) may be used as the method
argument in contrast
, or as the contr
argument or left-hand side of a spec
formula in lsmeans
.
pairwise.lsmc(levs, ...) revpairwise.lsmc(levs, ...) tukey.lsmc(levs, reverse = FALSE) poly.lsmc(levs, max.degree = min(6, k - 1)) trt.vs.ctrl.lsmc(levs, ref = 1) trt.vs.ctrl1.lsmc(levs, ...) trt.vs.ctrlk.lsmc(levs, ...) dunnett.lsmc(levs, ref = 1) consec.lsmc(levs, reverse = FALSE, ...) mean_chg.lsmc(levs, reverse = FALSE, ...) eff.lsmc(levs, ...) del.eff.lsmc(levs, ...)
levs |
Vector of factor levels |
... |
Additional arguments, ignored but needed to make these functions interchangeable |
max.degree |
The maximum degree of the polynomial contrasts in |
reverse |
Logical value to determine the direction of comparisons, e.g., pairwise (if |
ref |
Reference level (or control group) in |
Each contrast family has a default multiple-testing adjustment as noted below. These adjustments are often only approximate; for a more exacting adjustment, use the interfaces provided to glht
in the multcomp package.
pairwise.lsmc
, revpairwise.lsmc
, and tukey.lsmc
generate contrasts for all pairwise comparisons among least-squares means at the levels in levs
. The distinction is in which direction they are subtracted. For factor levels A, B, C, D, pairwise.lsmc
generates the comparisons A-B, A-C, A-D, B-C, B-D, and C-D, whereas revpairwise.lsmc
generates B-A, C-A, C-B, D-A, D-B, and D-C. tukey.lsmc
invokes pairwise.lsmc
or revpairwise.lsmc
depending on reverse
. The default multiplicity adjustment method is "tukey"
, which is approximate when the standard errors differ.
poly.lsmc
generates orthogonal polynomial contrasts, assuming equally-spaced factor levels. These are derived from the poly
function, but an ad hoc algorithm is used to scale them to integer coefficients that are (usually) the same as in published tables of orthogonal polynomial contrasts. The default multiplicity adjustment method is "none"
.
trt.vs.ctrl.lsmc
and its relatives generate contrasts for comparing one level (or the average over specified levels) with each of the other levels. The argument ref
should be the index(es) (not the labels) of the reference level(s). trt.vs.ctrl1.lsmc
is the same as trt.vs.ctrl
with a reference value of 1
, and trt.vs.ctrlk.lsmc
is the same as trt.vs.ctrl
with a reference value of length(levs)
. dunnett.lsmc
is the same as trt.vs.ctrl
.
The default multiplicity adjustment method is "dunnettx"
, a close approximation to the Dunnett adjustment.
consec.lsmc
and mean_chg.lsmc
are useful for contrasting treatments that occur in sequence. For a factor with levels A, B, C, D, E, consec.lsmc
generates the comparisons B-A, C-B, and D-C, while mean_chg.lsmc
generates the contrasts (B+C+D)/3 - A, (C+D)/2 - (A+B)/2, and D - (A+B+C)/3. With reverse = TRUE
, these differences go in the opposite direction.
eff.lsmc
and del.eff.lsmc
generate contrasts that compare each level with the average over all levels (in eff.lsmc
) or over all other levels (in del.eff.lsmc
). These differ only in how they are scaled. For a set of k lsmeans, del.eff.lsmc
gives weight 1 to one lsmean and weight -1/(k-1) to the others, while eff.lsmc
gives weights (k-1)/k and -1/k respectively, as in subtracting the overall lsmean from each lsmean.
The default multiplicity adjustment method is "fdr"
. This is a Bonferroni-based method and is slightly conservative; see p.adjust
A data.frame
, each column containing contrast coefficients for levs
.
The "desc"
attribute is used to label the results in lsmeans
,
and the "adjust"
attribute gives the default adjustment method for multiplicity.
You may create your own contrast functions, using these as guides. A function named mycontr.lsmc
may be invoked in lsmeans
via, e.g.,
lsmeans(\var{object}, mycontr ~ \var{factor})
The "desc"
, "adjust"
, and "offset"
attributes are optional; if present, these are passed to contrast
. If absent, the root name of the function is used as "desc"
, and no adjustment is requested for p values. See the examples.
Russell V. Lenth
### View orthogonal polynomials for 4 levels poly.lsmc(1:4) ### Setting up a custom contrast function helmert.lsmc <- function(levs, ...) { M <- as.data.frame(contr.helmert(levs)) names(M) <- paste(levs[-1],"vs earlier") attr(M, "desc") <- "Helmert contrasts" M } warp.lm <- lm(breaks ~ wool*tension, data = warpbreaks) lsmeans(warp.lm, helmert ~ tension | wool)