`algo.farrington.fitGLM.Rd`

The function fits a Poisson regression model (GLM) with mean predictor $$\log \mu_t = \alpha + \beta t$$ as specified by the Farrington procedure. If requested, Anscombe residuals are computed based on an initial fit and a 2nd fit is made using weights, where base counts suspected to be caused by earlier outbreaks are downweighted.

```
algo.farrington.fitGLM(response, wtime, timeTrend = TRUE,
reweight = TRUE, ...)
algo.farrington.fitGLM.fast(response, wtime, timeTrend = TRUE,
reweight = TRUE, ...)
algo.farrington.fitGLM.populationOffset(response, wtime, population,
timeTrend=TRUE,reweight=TRUE, ...)
```

- response
The vector of observed base counts

- wtime
Vector of week numbers corresponding to

`response`

- timeTrend
Boolean whether to fit the \(\beta t\) or not

- reweight
Fit twice -- 2nd time with Anscombe residuals

- population
Population size. Possibly used as offset, i.e. in

`algo.farrington.fitGLM.populationOffset`

the value`log(population)`

is used as offset in the linear predictor of the GLM: $$\log \mu_t = \log(\texttt{population}) + \alpha + \beta t$$ This provides a way to adjust the Farrington procedure to the case of greatly varying populations. Note: This is an experimental implementation with methodology not covered by the original paper.- ...
Used to catch additional arguments, currently not used.

Compute weights from an initial fit and rescale using
Anscombe based residuals as described in the
`anscombe.residuals`

function.

Note that `algo.farrington.fitGLM`

uses the `glm`

routine
for fitting. A faster alternative is provided by
`algo.farrington.fitGLM.fast`

which uses the `glm.fit`

function directly (thanks to Mikko Virtanen). This saves
computational overhead and increases speed for 500 monitored time
points by a factor of approximately two. However, some of the
routine `glm`

functions might not work on the output of this
function. Which function is used for `algo.farrington`

can be
controlled by the `control$fitFun`

argument.

an object of class GLM with additional fields `wtime`

,
`response`

and `phi`

. If the `glm`

returns without
convergence `NULL`

is returned.