Estimate Infectious Activity from Incidence and Serial Interval

Estimate Infectious Activity from Incidence and Serial Interval

estimate_activity(.data, incid, .t, serial_interval_mean, serial_interval_sd)

# S3 method for data.frame
estimate_activity(
  .data,
  incid = "trend",
  .t = "collection_date",
  serial_interval_mean = 6,
  serial_interval_sd = 4.17
)

# S3 method for covidmodel_rt
estimate_activity(
  .data,
  incid = ".incid",
  .t = ".t",
  serial_interval_mean = attr(.data, "serial_interval")[[1L]],
  serial_interval_sd = attr(.data, "serial_interval")[[2L]]
)

Arguments

.data

Daily incidence data in data frame or covidmodel_rt format

incid

Character. The column containing incidence data

.t

Character. The time column.

serial_interval_mean

Numeric. The average of the serial interval.

serial_interval_sd

Numeric. The standard deviation of the serial interval.