model_parameters.mira: Parameters from multiply imputed repeated analyses

In parameters: Processing of Model Parameters

Parameters from multiply imputed repeated analyses

Description

Format models of class mira, obtained from mice::width.mids(), or of class mipo.

Usage

## S3 method for class 'mipo'
model_parameters(
  model,
  ci = 0.95,
  exponentiate = FALSE,
  p_adjust = NULL,
  keep = NULL,
  drop = NULL,
  verbose = TRUE,
  ...
)

## S3 method for class 'mira'
model_parameters(
  model,
  ci = 0.95,
  exponentiate = FALSE,
  p_adjust = NULL,
  keep = NULL,
  drop = NULL,
  verbose = TRUE,
  ...
)

Arguments

model	An object of class mira or mipo.
ci	Confidence Interval (CI) level. Default to 0.95 (⁠95%⁠).
exponentiate	Logical, indicating whether or not to exponentiate the coefficients (and related confidence intervals). This is typical for logistic regression, or more generally speaking, for models with log or logit links. It is also recommended to use exponentiate = TRUE for models with log-transformed response values. Note: Delta-method standard errors are also computed (by multiplying the standard errors by the transformed coefficients). This is to mimic behaviour of other software packages, such as Stata, but these standard errors poorly estimate uncertainty for the transformed coefficient. The transformed confidence interval more clearly captures this uncertainty. For compare_parameters(), exponentiate = "nongaussian" will only exponentiate coefficients from non-Gaussian families.
p_adjust	Character vector, if not NULL, indicates the method to adjust p-values. See stats::p.adjust() for details. Further possible adjustment methods are "tukey", "scheffe", "sidak" and "none" to explicitly disable adjustment for emmGrid objects (from emmeans).
keep	Character containing a regular expression pattern that describes the parameters that should be included (for keep) or excluded (for drop) in the returned data frame. keep may also be a named list of regular expressions. All non-matching parameters will be removed from the output. If keep is a character vector, every parameter name in the "Parameter" column that matches the regular expression in keep will be selected from the returned data frame (and vice versa, all parameter names matching drop will be excluded). Furthermore, if keep has more than one element, these will be merged with an OR operator into a regular expression pattern like this: "(one|two|three)". If keep is a named list of regular expression patterns, the names of the list-element should equal the column name where selection should be applied. This is useful for model objects where model_parameters() returns multiple columns with parameter components, like in model_parameters.lavaan(). Note that the regular expression pattern should match the parameter names as they are stored in the returned data frame, which can be different from how they are printed. Inspect the ⁠$Parameter⁠ column of the parameters table to get the exact parameter names.
drop	See keep.
verbose	Toggle warnings and messages.
...	Arguments passed to or from other methods.

Details

model_parameters() for objects of class mira works similar to summary(mice::pool()), i.e. it generates the pooled summary of multiple imputed repeated regression analyses.

Examples

library(parameters)
data(nhanes2, package = "mice")
imp <- mice::mice(nhanes2)
fit <- with(data = imp, exp = lm(bmi ~ age + hyp + chl))
model_parameters(fit)

# model_parameters() also works for models that have no "tidy"-method in mice
data(warpbreaks)
set.seed(1234)
warpbreaks$tension[sample(1:nrow(warpbreaks), size = 10)] <- NA
imp <- mice::mice(warpbreaks)
fit <- with(data = imp, expr = gee::gee(breaks ~ tension, id = wool))

# does not work:
# summary(mice::pool(fit))

model_parameters(fit)


# and it works with pooled results
data("nhanes2", package = "mice")
imp <- mice::mice(nhanes2)
fit <- with(data = imp, exp = lm(bmi ~ age + hyp + chl))
pooled <- mice::pool(fit)

model_parameters(pooled)

parameters documentation built on Oct. 18, 2024, 5:13 p.m.