Using update
In update
, the names in …
are partially matched against those that are valid, and if a match is found, it adds or replaces the current setting. The valid names are
nesting
(named list
) specifies the nesting structure. The names are those of nested factors, and the elements are character vectors of the factors they are nested in. See the nesting
argument and Details section of ref.grid
. The current nesting structure is displayed by link{str}
.
tran
, tran2
(list
or character
) specifies the transformation which, when inverted, determines the results displayed by summary
, predict
, or lsmip
when type="response"
. The value may be the name of a standard transformation from make.link
or additional ones supported by name, such as log2
; or, for a custom transformation, a list
containing at least the functions linkinv
(the inverse of the transformation) and mu.eta
(the derivative thereof). The make.tran
function returns such lists for a number of popular transformations. See the help page of make.tran
for details as well as information on the additional named transformations that are supported. tran2
is just like tran
except it is a second transformation (i.e., a response transformation in a generalized linear model).
tran.mult
Multiple for tran
. For example, for the response transformation 2*sqrt(y) (or sqrt(y) + sqrt(y + 1), for that matter), we should have tran = "sqrt"
and tran.mult = 2
. If absent, a multiple of 1 is assumed.
estName
(character
) is the column label used for displaying predictions or LS means.
inv.lbl
(character)
) is the column label to use for predictions or LS means when type="response"
.
by.vars
(character)
vector or NULL
) the variables used for grouping in the summary, and also for defining subfamilies in a call to contrast
.
pri.vars
(character
vector) are the names of the grid variables that are not in by.vars
. Thus, the combinations of their levels are used as columns in each table produced by summary
.
alpha
(numeric) is the default significance level for tests, in summary
as well as cld
and plot
when intervals = TRUE
adjust
(character)
) is the default for the adjust
argument in summary
.
estType
(character
) is the type of the estimate. It should match one of c("prediction","contrast","pairs"). This is used along with "adjust"
to determine appropriate adjustments to P values and confidence intervals.
famSize
(integer) is the nmeans
parameter for ptukey
when adjust="tukey"
.
infer
(logical
vector of length 2) is the default value of infer
in summary
.
level
(numeric) is the default confidence level, level
, in summary
df
(numeric) overrides the default degrees of freedom with a specified single value.
null
(numeric) null hypothesis for summary
or test
(taken to be zero if missing).
side
(numeric or character) side
specification for for summary
or test
(taken to be zero if missing).
delta
(numeric) delta
specification for summary
or test
(taken to be zero if missing).
predict.type
(character) sets the default method of displaying predictions in summary
, predict
, and lsmip
. Valid values are "link"
(with synonyms "lp"
and "linear"
), or "response"
.
avgd.over
(character)
vector) are the names of the variables whose levels are averaged over in obtaining marginal averages of predictions, i.e., LS means. Changing this might produce a misleading printout, but setting it to character(0)
will suppress the “averaged over” message in the summary.
initMesg
(character
) is a string that is added to the beginning of any annotations that appear below the summary
display.
methDesc
(character
) is a string that may be used for creating names for a list of lsmobj
objects.
(any slot name)If the name matches an element of slotNames(object)
, that slot is replaced by the supplied value, if it is of the required class (otherwise an error occurs). Note that all the other possibilities above refer to elements of misc
; hence, you probably don't want to replace misc
itself. The user must be very careful in replacing slots because they are interrelated; for example, the levels
and grid
slots must involve the same variable names, and the lengths and dimensions of grid
, linfct
, bhat
, and V
must conform.
Using lsm.options
In lsm.options
, we may set or change the default values for the above attributes in the lsmeans
option list(see options
). Currently, the following elements of this list are used if specified:
ref.grid
A named list
of defaults for objects created by ref.grid
. This could affect other objects as well. For example, if lsmeans
is called with a fitted model object, it calls ref.grid
and this option will affect the resulting lsmobj
object.
lsmeans
A named list
of defaults for objects created by lsmeans
(or lstrends
).
contrast
A named list
of defaults for objects created by contrast
(or pairs
).
summary
A named list
of defaults used by the methods summary
, predict
, and lsmip
. The only option that can affect the latter two is "predict.method"
.
estble.tol
Tolerance for determining estimability in rank-deficient cases. If absent, the value in defaults.lsm$estble.tol)
is used.
- (others)
Other options may be accessed by support code for particular model classes (see models
). For example, the lmer.df
, disable.pbkrtest
, and pbkrtest.limit
options affect how degrees of freedom are computed for lmerMod
objects (lme4 package).