This function "pools" (i.e. combines) model parameters in a similar fashion
as mice::pool()
. However, this function pools parameters from
parameters_model
objects, as returned by
model_parameters()
.
Usage
pool_parameters(
x,
exponentiate = FALSE,
effects = "fixed",
component = "conditional",
verbose = TRUE,
...
)
Arguments
- x
A list of
parameters_model
objects, as returned bymodel_parameters()
, or a list of model-objects that is supported bymodel_parameters()
.- 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. Forcompare_parameters()
,exponentiate = "nongaussian"
will only exponentiate coefficients from non-Gaussian families.- effects
Should parameters for fixed effects (
"fixed"
), random effects ("random"
), or both ("all"
) be returned? Only applies to mixed models. May be abbreviated. If the calculation of random effects parameters takes too long, you may useeffects = "fixed"
.- component
Should all parameters, parameters for the conditional model, for the zero-inflation part of the model, or the dispersion model be returned? Applies to models with zero-inflation and/or dispersion component.
component
may be one of"conditional"
,"zi"
,"zero-inflated"
,"dispersion"
or"all"
(default). May be abbreviated.- verbose
Toggle warnings and messages.
- ...
Currently not used.
Details
Averaging of parameters follows Rubin's rules (Rubin, 1987, p. 76). The pooled degrees of freedom is based on the Barnard-Rubin adjustment for small samples (Barnard and Rubin, 1999).
Note
Models with multiple components, (for instance, models with zero-inflation,
where predictors appear in the count and zero-inflation part) may fail in
case of identical names for coefficients in the different model components,
since the coefficient table is grouped by coefficient names for pooling. In
such cases, coefficients of count and zero-inflation model parts would be
combined. Therefore, the component
argument defaults to
"conditional"
to avoid this.
Some model objects do not return standard errors (e.g. objects of class
htest
). For these models, no pooled confidence intervals nor p-values
are returned.
References
Barnard, J. and Rubin, D.B. (1999). Small sample degrees of freedom with multiple imputation. Biometrika, 86, 948-955. Rubin, D.B. (1987). Multiple Imputation for Nonresponse in Surveys. New York: John Wiley and Sons.
Examples
# example for multiple imputed datasets
if (require("mice")) {
data("nhanes2")
imp <- mice(nhanes2, printFlag = FALSE)
models <- lapply(1:5, function(i) {
lm(bmi ~ age + hyp + chl, data = complete(imp, action = i))
})
pool_parameters(models)
# should be identical to:
m <- with(data = imp, exp = lm(bmi ~ age + hyp + chl))
summary(pool(m))
}
#> term estimate std.error statistic df p.value
#> 1 (Intercept) 18.14256305 3.54562901 5.116881 11.625350 0.0002813879
#> 2 age40-59 -6.15715380 2.19792337 -2.801351 5.969005 0.0312810653
#> 3 age60-99 -7.72866592 2.45997959 -3.141760 6.642762 0.0174969755
#> 4 hypyes 2.46673562 2.07396774 1.189380 6.147560 0.2781911871
#> 5 chl 0.06028557 0.02078061 2.901050 10.206904 0.0154916183