Access epidemiological delay distributions

  • Use {epiparameter} to access the literature catalogue of epidemiological delay distributions.
  • Use epiparameter_db() to select single delay distributions.
  • Use parameter_tbl() for an overview of multiple delay distributions.
  • Reuse known estimates for unknown disease in the early stage of an outbreak when no contact tracing data is available.

Quantifying transmission

  • Transmission metrics can be estimated from case data after accounting for delays
  • Uncertainty can be accounted for in delay distributions

Use delay distributions in analysis

  • Use distribution functions with <epidist> objects to get summary statistics and informative parameters for public health interventions like the Window for contact tracing and Length of quarantine.
  • Use discretise() to convert continuous to discrete delay distributions.
  • Use {epiparameter} to get reporting delays required in transmissibility estimates.

Create a short-term forecast

  • We can create short-term forecasts by making assumptions about the future behaviour of the reproduction number
  • Incomplete case reporting can be accounted for in estimates

Estimation of outbreak severity

  • Use cfr to estimate severity

  • Use cfr_static() to estimate the overall CFR with the latest data available.

  • Use cfr_rolling() to show what the estimated CFR would be on each day of the outbreak.

  • Use the delay_density argument to adjust the CFR by the corresponding delay distribution.

Account for superspreading

  • Use epicontacts to calculate the number of secondary cases cause by a particular individual from linelist and contact data.
  • Use fitdistrplus to empirically estimate the offspring distribution from the number of secondary cases distribution.
  • Use {superspreading} to estimate the probability of having clusters of a given size from primary cases and inform contact tracing efforts.

Simulate transmission chains

  • Use epichains to simulate the large outbreak potential of diseases with overdispersed offspring distributions.