MuMIn (version 1.48.4)

model.avg: Model averaging

Description

Model averaging based on an information criterion.

Usage

model.avg(object, ..., revised.var = TRUE)
# S3 method for default
model.avg(object, ..., beta = c("none", "sd", "partial.sd"),
  rank = NULL, rank.args = NULL, revised.var = TRUE,
  dispersion = NULL, ct.args = NULL)
# S3 method for model.selection
model.avg(object, subset, fit = FALSE, ..., revised.var = TRUE)

Value

An object of class "averaging" is a list with components:

msTable

a data.frame with log-likelihood, IC, Δ_IC and ‘Akaike weights’ for the component models. Its attribute "term.codes" is a named vector with numerical representation of the terms in the row names of msTable.

coefficients

a matrix of model-averaged coefficients. “full” coefficients in the first row, “subset” coefficients in the second row. See ‘Note’

coefArray

a 3-dimensional array of component models' coefficients, their standard errors and degrees of freedom.

sw

object of class sw containing per-model term sum of model weights over all of the models in which the term appears.

formula

a formula corresponding to the one that would be used in a single model. The formula contains only the averaged (fixed) coefficients.

call

the matched call.

The object has the following attributes:

rank

the rank function used.

modelList

optionally, a list of all component model objects. Only if the object was created with model objects (and not model selection table).

beta

Corresponds to the function argument.

nobs

number of observations.

revised.var

Corresponds to the function argument.

Arguments

object

a fitted model object or a list of such objects, or a "model.selection" object. See ‘Details’.

...

for default method, more fitted model objects. Otherwise, arguments that are passed to the default method.

beta

indicates whether and how the component models' coefficients should be standardized. See the argument's description in dredge.

rank

optionally, a rank function (returning an information criterion) to use instead of AICc, e.g. BIC or QAIC, may be omitted if object is a model list returned by get.models or a "model.selection" object. See ‘Details’.

rank.args

optional list of arguments for the rank function. If one is an expression, an x within it is substituted with a current model.

revised.var

logical, indicating whether to use the revised formula for standard errors. See par.avg.

dispersion

the dispersion parameter for the family used. See summary.glm. This is used currently only with glm, is silently ignored otherwise.

ct.args

optional list of arguments to be passed to coefTable (besides dispersion).

subset

see subset method for "model.selection" object.

fit

if TRUE, the component models are fitted using get.models. See ‘Details’.

Author

Kamil Bartoń

Details

model.avg may be used either with a list of models or directly with a model.selection object (e.g. returned by dredge). In the latter case, the models from the model selection table are not evaluated unless the argument fit is set to TRUE or some additional arguments are present (such as rank or dispersion). This results in a much faster calculation, but has certain drawbacks, because the fitted component model objects are not stored, and some methods (e.g. predict, fitted, model.matrix or vcov) would not be available with the returned object. Otherwise, get.models is called prior to averaging, and ... are passed to it.

For a list of model types that are accepted see list of supported models.

rank is found by a call to match.fun and typically is specified as a function or a symbol or a character string specifying a function to be searched for from the environment of the call to lapply. rank must be a function able to accept model as a first argument and must always return a numeric scalar.

Several standard methods for fitted model objects exist for class averaging, including summary, predict, coef, confint, formula, and vcov.

coef, vcov, confint and coefTable accept argument full that if set to TRUE, the full model-averaged coefficients are returned, rather than subset-averaged ones (when full = FALSE, being the default).

logLik returns a list of logLik objects for the component models.

References

Burnham, K. P. and Anderson, D. R. 2002 Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. New York, Springer-Verlag.

Lukacs, P. M., Burnham K. P. and Anderson, D. R. 2009 Model selection bias and Freedman’s paradox. Annals of the Institute of Statistical Mathematics 62, 117–125.

See Also

See par.avg for more details of model-averaged parameter calculation.

dredge, get.models
AICc has examples of averaging models fitted by REML.

modavg in package AICcmodavg, and coef.glmulti in package glmulti also perform model averaging.

Examples

# Example from Burnham and Anderson (2002), page 100:
fm1 <- lm(y ~ ., data = Cement, na.action = na.fail)
(ms1 <- dredge(fm1))

#models with delta.aicc < 4
summary(model.avg(ms1, subset = delta < 4))

#or as a 95% confidence set:
avgmod.95p <- model.avg(ms1, cumsum(weight) <= .95)
confint(avgmod.95p)

if (FALSE) {
# The same result, but re-fitting the models via 'get.models'
confset.95p <- get.models(ms1, cumsum(weight) <= .95)
model.avg(confset.95p)

# Force re-fitting the component models
model.avg(ms1, cumsum(weight) <= .95, fit = TRUE)
# Models are also fitted if additional arguments are given
model.avg(ms1, cumsum(weight) <= .95, rank = "AIC")
}

if (FALSE) {
# using BIC (Schwarz's Bayesian criterion) to rank the models
BIC <- function(x) AIC(x, k = log(length(residuals(x))))
model.avg(confset.95p, rank = BIC)
# the same result, using AIC directly, with argument k
# 'x' in a quoted 'rank' argument is substituted with a model object
# (in this case it does not make much sense as the number of observations is
# common to all models)
model.avg(confset.95p, rank = AIC, rank.args = alist(k = log(length(residuals(x)))))
}