surveillance: twinstim_update – R documentation

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twinstim_update

update-method for "twinstim"

Description

Update and (by default) re-fit a "twinstim". This method is especially useful if one wants to add the model environment (which is required for some methods) to a fitted model object a posteriori.

Usage

## S3 method for class 'twinstim'
update(object, endemic, epidemic,
       control.siaf, optim.args, model,
       ..., use.estimates = TRUE, evaluate = TRUE)

Arguments

`object`	a previous `"twinstim"` fit.
`endemic, epidemic`	changes to the formulae – see `update.formula` and `twinstim`.
`control.siaf`	a list (see `twinstim`) to replace the given elements in the original `control.siaf` list. If `NULL`, the original list of control arguments is removed from the call, i.e., the defaults are used in `twinstim`.
`optim.args`	see `twinstim`. If a list, it will modify the original `optim.args` using `modifyList`.
`model`	see `twinstim`. If this is the only argument to update, re-fitting is cleverly circumvented. Enriching the fit by the model environment is, e.g., required for `intensityplot.twinstim`.
`...`	Additional arguments to the call, or arguments with changed values. If `start` values are specified, they need to be in the same format as in the original call `object$call$start`, which is either a named list of named numeric vectors or a named numeric vector; see the argument description in `twinstim`.
`use.estimates`	logical indicating if the estimates of `object` should be used as initial values for the new fit (in the `start` argument of `twinstim`). Defaults to `TRUE`.
`evaluate`	If `TRUE` (default), evaluate the new call else return the call.

Value

If evaluate = TRUE the re-fitted object, otherwise the updated call.

Author(s)

Sebastian Meyer

Inspiration and some pieces of code originate from update.default by the R Core Team.

Examples

data("imdepi", "imdepifit")

## add another epidemic covariate
## (but fix siaf-parameter so that this example runs quickly)
imdepifit2 <- update(imdepifit, epidemic = ~. + log(popdensity),
                     optim.args = list(fixed="e.siaf.1"))

## compare by AIC
AIC(imdepifit, imdepifit2)

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

v1.19.1

GPL-2

Authors

Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>), Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>), Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Saban<e9>s Bov<e9> [ctb], Ma<eb>lle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)

Initial release

2021-03-30