Function reference

All functions

Custom-class

This class is a container for the parameterization using external data.

Emission-class

This class is a generic container for the model used for excess count detection, which defines the probability distributions.

Emission()

Create an Emission object for excess count detection

EmissionGLMNegBinom-class

This class defines the Emission function for Negative Binomial GLMs.

EmissionGLMPoisson-class

This class defines the Emission function for Poisson GLMs.

excodeFamily-class

This class is a generic container for a family of probability distributions

excodeFamily()

Create a family of probability distributions for excess count detection.

excodeFormula-class

This class is a generic container for a formula which specifies the model used for excess count detection.

excodeFormula()

Create a formula of the model for excess count detection

excodeModel-class

This class is a generic container for the model used for outbreak detection

excodeModel()

Create a model for excess count detection

FarringtonNoufaily-class

This class is a container for the parameterization of the FarringtonNoufaily models.

Harmonic-class

This class is a container for the parameterization of the Harmonic models.

Mean-class

This class is a container for the parameterization of the Mean models.

mort_df_germany

German all-cause mortality data

MultiState-class

This class is a container for the parameterization of a MultiState model.

NegBinom-class

This class is a generic container for a family of Negative Binomial distributions

plot(<excodeModel>,<ANY>)

Summary of an excodeModel.

plot_model()

Plot sts object with excode results

Poisson-class

This class is a generic container for a family of Poisson distributions

run_excode()

Detect Excess Counts in Epidemiological Time Series

sarscov2_df

SARS-CoV-2 infections in Berlin-Neukölln (Germany)

shadar_df

Salmonella Hadar cases in Germany 2001-2006

snewport_df

Salmonella Newport cases in Germany 2004-2014

Splines-class

This class is a container for the parameterization of Spline models. This class is experimental and not recommended for use!

summary(<excodeModel>)

Summary of an excodeModel.