Description Usage Arguments Examples

View source: R/estpars_function.R

This function computes the set up to run the TSIR model, i.e. reconstructs susecptibles and estimates beta and alpha. This can be plugged into simulatetsir.

1 2 3 4 |

`data` |
The data frame containing cases and interpolated births and populations. |

`xreg` |
The x-axis for the regression. Options are 'cumcases' and 'cumbirths'. Defaults to 'cumcases'. |

`IP` |
The infectious period in weeks. This should be the same as your timestep. Defaults to 2 weeks. |

`seasonality` |
The type of contact to use. Options are standard for 52/IP point contact or schoolterm for just a two point on off contact or none for a single contact parameter. Defaults to standard. |

`regtype` |
The type of regression used in susceptible reconstruction. Options are 'gaussian', 'lm' (linear model), 'spline' (smooth.spline with 2.5 degrees freedom), 'lowess' (with f = 2/3, iter = 1), 'loess' (degree 1), and 'user' which is just a user inputed vector. Defaults to 'gaussian' and if that fails then defaults to loess. |

`sigmamax` |
The inverse kernal width for the gaussian regression. Default is 3. Smaller, stochastic outbreaks tend to need a lower sigma. |

`family` |
The family in the GLM regression. One can use any of the GLM ones, but the options are essentially 'poisson' (with link='log'), 'gaussian' (with link='log' or 'identity'), or 'quasipoisson' (with link='log'). Default is 'gaussian'. |

`link` |
The link function used with the glm family. Options are link='log' or 'identity'. Default is 'identity'. to include some bayesian approaches. For 'bayesglm' we use a gaussian prior with mean 1e-4. |

`userYhat` |
The inputed regression vector if regtype='user'. Defaults to NULL. |

`alpha` |
The mixing parameter. Defaults to NULL, i.e. the function estimates alpha. |

`sbar` |
The mean number of susceptibles. Defaults to NULL, i.e. the function estimates sbar. |

`printon` |
Whether to show diagnostic prints or not, defaults to FALSE. |

1 2 3 4 5 6 7 8 9 | ```
## Not run:
require(kernlab)
London <- twentymeas[["London"]]
parms <- estpars(London)
names(parms)
sim <- simulatetsir(London,parms=parms,inits.fit=FALSE)
plotres(sim)
## End(Not run)
``` |

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