Returns a data.frame summarizing a Covidestim model run. Note that if runOptimizer.covidestim is used, all *.(lo|hi) variables will be NA-valued, because BFGS does not generate confidence intervals.

# S3 method for covidestim_result
summary(ccr, include.before = TRUE, index = FALSE)



A covidestim_result object


A logical scalar. Include estimations that fall in the period before the first day of input data? (This period is of length ndays_before as passed to covidestim). If TRUE, any elements of variables which do not have values for this "before" period will be represented as NA.


A logical scalar. If TRUE, will include a variable index in the output, with range 1:(ndays_before + ndays).


A data.frame with the following variables:

  • date

  • cases.fitted, cases.fitted.lo, cases.fitted.hi: Median and 95% interval around fitted case data.

  • cum.incidence, cum.incidence.lo, cum.incidence.hi: Median and 95% interval around cumulative incidence data.

  • deaths.fitted, deaths.fitted.lo, deaths.fitted.hi: Median and 95% interval around fitted deaths data.

  • deaths, deaths.lo, deaths.hi: Median and 95% interval around estimated deaths/day, by date of death.

  • infections, infections.lo, infections.hi: Median and 95% interval around estimated infections/day, by date of infection.

  • severe, severe.lo, severe.hi: Median and 95% interval around the number of individuals who transitioned into the "severe" health state on a particular day. The "severe" state is defined as disease that would merit hospitalization.

  • symptomatic, symptomatic.lo, symptomatic.hi: Median and 95% interval around the estimate of the quantity of individuals who became symtomatic on a particular day.

  • data.available: TRUE/FALSE for whether input data was available on that particular day.

  • Rt, Rt.lo, Rt.hi: Estimate of the effective reproductive number (Rt), with 95% CIs.

  • sero.positive, sero.positive.lo, sero.positive.hi: Estimate of the number of seropositive individuals, with 95% CIs.

  • pop.infectiousness, pop.infectiousness.lo, pop.infectiousness.hi: Estimate of the relative level of viral shedding in the community, with 95% CIs.