Package index

All functions

Custom-class

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

Emission-class

Emission Class

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.

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.

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

Poisson-class

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

compute_baseline_state()

Update EXCODE model by setting baseline states in surv_ts

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

excodeFormula Class

excodeFormula()

Create a formula for excess count detection

excodeModel-class

excodeModel Class

excodeModel()

Create a model for excess count detection

init_excode()

Initialize a multi-state EXCODE model from a surveillance time series

mort_df_germany

German all-cause mortality data

plot_excode_summary()

Plot EXCODE summary diagnostics across multiple panels

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

summary(<excodeModel>)

Summary of an excodeModel