Estimates the maximum likelihood estimate and 95% confidence interval of a corrected severity, using the total cases and total cases with known outcomes, where the latter replaces the total number of deaths in the standard (naive) severity definition. We use a binomial likelihood, approximated by a Poisson likelihood for large samples.
Usage
.estimate_severity(
total_cases,
total_deaths,
total_outcomes,
poisson_threshold,
p_mid = total_deaths/round(total_outcomes)
)
Arguments
- total_cases
The total number of cases observed over the period of an outbreak of interest. The total number of cases must be greater than or equal to the total number of deaths.
- total_deaths
The total number of deaths observed over the period of an outbreak of interest. The total number of deaths must be less than or equal to the total number of cases.
- total_outcomes
The total number of outcomes expected to be observed over the period of an outbreak of interest. See
estimate_outcomes()
.- poisson_threshold
The case count above which to use Poisson approximation. Set to 100 by default. Must be > 0.
- p_mid
The initial severity estimate, which is used to determine the likelihood approximation used when
total_cases
>poisson_threshold
. Defaults tototal_deaths / round(total_outcomes)
.
Value
A <data.frame>
with one row and three columns for the maximum
likelihood estimate and 95% confidence interval of the corrected severity
estimates, named "severity_estimate", "severity_low", and "severity_high".
Details
Special cases
When any two of
total_cases
,total_deaths
, ortotal_outcomes
are 0, the estimate and confidence intervals cannot be calculated and the output<data.frame>
contains onlyNA
s.When
total_outcomes <= total_deaths
, estimate and confidence intervals cannot be reliably calculated and are returned asNA
.