emm_options {emmeans} | R Documentation |
Use emm_options
to set or change various options that are used in
the emmeans package. These options are set separately for different contexts in
which emmGrid
objects are created, in a named list of option lists.
emm_options(...) get_emm_option(x, default = emm_defaults[[x]]) emm_defaults
... |
Option names and values (see Details) |
x |
Character value - the name of an option to be queried |
default |
Value to return if |
An object of class list
of length 15.
Currently, the following main list entries are supported:
ref_grid
A named list
of defaults for objects created by
ref_grid
. This could affect other objects as well. For example,
if emmeans
is called with a fitted model object, it calls
ref_grid
and this option will affect the resulting emmGrid
object.
emmeans
A named list
of defaults for objects created by
emmeans
or emtrends
.
contrast
A named list
of defaults for objects created by
contrast.emmGrid
or pairs.emmGrid
.
summary
A named list
of defaults used by the methods
summary.emmGrid
, predict.emmGrid
, test.emmGrid
,
confint.emmGrid
, and emmip
. The only option that can
affect the latter four is "predict.method"
.
graphics.engine
A character value matching
c("ggplot", "lattice")
, setting the default engine to use in
emmip
and plot.emmGrid
. Defaults to "ggplot"
.
msg.interaction
A logical value controlling whether or not
a message is displayed when emmeans
averages over a factor involved
in an interaction. It is probably not appropriate to do this, unless
the interaction is weak. Defaults to TRUE
.
msg.nesting
A logical value controlling whether or not to
display a message when a nesting structure is auto-detected. The existence
of such a structure affects computations of EMMs. Sometimes, a nesting
structure is falsely detected – namely when a user has omitted some
main effects but included them in interactions. This does not change the
model fit, but it produces a different parameterization that is picked
up when the reference grid is constructed. Defaults to TRUE
.
simplify.names
A logical value controlling whether to
simplify (when possible) names in the model formula that refer to datasets –
for example, should we simplify a predictor name like “data$trt
”
to just “trt
”? Defaults to TRUE
.
opt.digits
A logical value controlling the precision with which
summaries are printed. If TRUE
(default), the number of digits
displayed is just enough to reasonably distinguish estimates from the ends
of their confidence intervals; but always at least 3 digits. If
FALSE
, the system value getOption("digits")
is used.
Some other options have more specific purposes:
estble.tol
Tolerance for determining estimability in
rank-deficient cases. If absent, the value in emm_defaults$estble.tol)
is used.
save.ref_grid
Logical value of TRUE
if you wish the
latest reference grid created to be saved in .Last.ref_grid
lme4::lmerMod
modelsOptions lmer.df
,
disable.pbkrtest
, pbkrtest.limit
, disable.lmerTest
,
and lmerTest.limit
options affect how degrees of freedom are computed for lmerMod
objects
produced by the lme4 package). See that section of the "models" vignette
for details.
emm_options
returns the current options (same as the result
of getOption("emmeans")) – invisibly, unless called with no arguments.
get_emm_option
returns the currently stored option for x
,
or its default value if not found.
## Not run: emm_options(ref_grid = list(level = .90), contrast = list(infer = c(TRUE,FALSE)), estble.tol = 1e-6) # Sets default confidence level to .90 for objects created by ref.grid # AS WELL AS emmeans called with a model object (since it creates a # reference grid). In addition, when we call 'contrast', 'pairs', etc., # confidence intervals rather than tests are displayed by default. ## End(Not run) ## Not run: emm_options(disable.pbkrtest = TRUE) # This forces use of asymptotic methods for lmerMod objects. # Set to FALSE or NULL to re-enable using pbkrtest. ## End(Not run) # See tolerance being used for determining estimability get_emm_option("estble.tol")