Read case data

---

• Use {rio}, {io}, {readr} and {ImportExport} to read data from individual files.
• Use {readepi} to read data form HIS APIs and RDBMS.

Clean and validate

---

• Use {cleanepi} package to clean and standardize epidemic and outbreak data
• Use linelist to tagg, validate, and prepare case data for downstream analysis.

Aggregate and visulaize

---

• Use {simulist} package to generate synthetic outbreak data
• Use incidence2 package to aggregate case data based on a date event, and produce epidemic curves.

Simple analysis

---

• Use i2extras to:
  • fit epi-curve using either Poisson or NB distributions,
    
  • calculate exponential growth or decline of cases,
  • find peak time, and
  • computing moving average of cases in specified time window.

Access epidemiological delay distributions

---

• Use {epiparameter} to access the literature catalogue of epidemiological delay distributions.
• Use epidist_db() to select single delay distributions.
• Use list_distributions() 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.