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Extract Included Realizations from an amerasfit Object

included_realizations.Rd

Extracts the indices of dose realizations included in model averaging for FMA and/or BMA results of a fitted amerasfit object. Realizations are excluded from FMA if the optimization did not converge or the Hessian was not positive definite.

Usage

included_realizations(x, ...)

# S3 method for class 'amerasfit'
included_realizations(x,
                              methods = c("FMA", "BMA"),
                              ...)

Arguments

x

A fitted model object of class amerasfit, as returned by ameras, with FMA and/or BMA results present.

methods

Character vector specifying which method(s) to extract included realizations for. One or both of "FMA" and "BMA". Defaults to both. Only methods that were run are returned.

...

Additional arguments, currently unused.

Value

If a single method is requested or only one method was run, an integer vector of indices of the included dose realizations. If both FMA and BMA results are present and both are requested, a named list with elements FMA and BMA, each containing an integer vector of included realization indices.

Details

For FMA, realizations are excluded if the optimization did not converge or the Hessian was not invertible or not positive definite. If more than 20% of realizations are excluded, a warning is issued during fitting.

For BMA, all realizations are included by default. A subset of realizations can be specified via the included.replicates.BMA argument to ameras, for example by passing the indices returned by included_realizations(fit, methods="FMA") from a prior FMA fit.

See also

ameras, Rhat.amerasfit

Examples

# \donttest{
data("data", package="ameras")
dosevars <- paste0("V", 1:10)

## FMA only
fit <- ameras(Y.binomial ~ dose(all_of(dosevars), model="ERR"),
              data=data, family="binomial", methods="FMA")
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found
included_realizations(fit)
#> Error: object 'fit' not found
length(included_realizations(fit))
#> Error: object 'fit' not found

## Both FMA and BMA
fit2 <- ameras(Y.binomial ~ dose(all_of(dosevars), model="ERR"),
               data=data, family="binomial", methods=c("FMA", "BMA"))
#> Note: BMA may require extensive computation time
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found
included_realizations(fit2)
#> Error: object 'fit2' not found
included_realizations(fit2, methods="FMA")
#> Error: object 'fit2' not found
included_realizations(fit2, methods="BMA")
#> Error: object 'fit2' not found
# }