update.emmGrid: Update an `emmGrid` object

Description

Objects of class emmGrid contain several settings that affect such things as what arguments to pass to summary.emmGrid. The update method allows safer management of these settings than by direct modification of its slots.

Usage

# S3 method for emmGrid
update(object, ..., silent = FALSE)

Arguments

object

An emmGrid object

...

Options to be set. These must match a list of known options (see Details)

silent

Logical value. If FALSE (the default), a message is displayed if any options are not matched. If TRUE, no messages are shown.

Value

an updated emmGrid object.

Details

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

tran, tran2: (list or character) specifies the transformation which, when inverted, determines the results displayed by summary.emmGrid, predict.emmGrid, or emmip 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 EMMs.
inv.lbl: (character)) is the column label to use for predictions or EMMs 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.emmGrid.
alpha: (numeric) is the default significance level for tests, in summary.emmGrid as well as CLD.emmGrid and plot.emmGrid when intervals = TRUE
adjust: (character)) is the default for the adjust argument in summary.emmGrid.
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.emmGrid.
level: (numeric) is the default confidence level, level, in summary.emmGrid
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 or type: (character) sets the default method of displaying predictions in summary.emmGrid, predict.emmGrid, and emmip. 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., estimated marginal 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.emmGrid display.
methDesc: (character) is a string that may be used for creating names for a list of emmGrid objects.
nesting: (Character or named list) specifies the nesting structure. See “Recovering or overriding model information” in the documentation for ref_grid. The current nesting structure is displayed by str.emmGrid.
(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 other options above are saved in the misc slot; hence, you probably don't want to replace that slot. 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.

Examples

Run this code

# NOT RUN {
# Using an already-transformed response:
mypigs <- transform(pigs, logconc = log(pigs$conc))
mypigs.lm <- lm(logconc ~ source + factor(percent), data = mypigs)

# Reference grid that knows about the transformation:
mypigs.rg <- update(ref_grid(mypigs.lm), tran = "log", 
                    predict.type = "response")
emmeans(mypigs.rg, "source")
# }