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.
- fit epi-curve using either Poisson or
NB distributions,
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.