surveillance: twinSIR_profile – R documentation

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twinSIR_profile

Profile Likelihood Computation and Confidence Intervals

Description

Function to compute estimated and profile likelihood based confidence intervals. Computations might be cumbersome! There is a simple plot-method for the result.

Usage

## S3 method for class 'twinSIR'
profile(fitted, profile, alpha = 0.05,
        control = list(fnscale = -1, factr = 10, maxit = 100), ...)

Arguments

`fitted`	an object of class `"twinSIR"`.
`profile`	a list with elements being numeric vectors of length 4. These vectors must have the form `c(index, lower, upper, gridsize)`. `index`: index of the parameter to be profiled in the vector `coef(fitted)`. `lower, upper`: lower/upper limit of the grid on which the profile log-likelihood is evaluated. Can also be `NA` in which case `lower/upper` equals the lower/upper bound of the respective 0.3 % Wald confidence interval (+-3*se). `gridsize`: grid size of the equally spaced grid between lower and upper. Can also be 0 in which case the profile log-likelihood for this parameter is not evaluated on a grid.
`alpha`	(1-alpha)100%* profile likelihood based confidence intervals are computed. If `alpha <= 0`, then no confidence intervals are computed.
`control`	control object to use in `optim` for the profile log-likelihood computations.
`...`	unused (argument of the generic).

Value

a list with profile log-likelihood evaluations on the grid and highest likelihood and Wald confidence intervals. The argument profile is also returned. The result has class "profile.twinSIR", for which a simple (undocumented) plot-method is available.

Author(s)

Michael Höhle and Sebastian Meyer

Examples

data("hagelloch")
fit <- twinSIR(~ household, data = hagelloch)
gridsize <- if (interactive()) 35 else 5  # for fast tests
prof <- profile(fit, list(c(1, NA, NA, gridsize)))
prof$ci.hl
plot(prof)

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