Fixed distributions on reporting delays

This function returns a keyed list of mean values for the gamma distribution of delays related reporting of cases and deaths. Called with no arguments, the default values are returned. Custom hyperpriors can be specified by passing values for the parameters specified below. The return value of this function must be added to a covidestim object using the addition operator (see examples).

priors_reporting_delays(
  cas_rep_delay = c(2.2, 1 * 7),
  die_rep_delay = c(2.2, 1 * 7)
)

Arguments

cas_rep_delay

A two-element numeric vector containing the mean shape and rate for a gamma distribution describing the delay (in days) in case reporting. Shape and rate are parameterized with a lognormal prior where the log of the input value is the median and the variance is 0.5. Based on average delay reported in Santa Clara County, CA on 8 April 2020.

die_rep_delay

A two-element numeric vector containing the mean shape and rate for a gamma distribution describing delay (in days) in death reporting. Shape and rate are parameterized with a lognormal prior where the log of the input value is the median and the variance is 0.5. Based on average delay reported in Santa Clara County, CA on 8 April 2020.

Value

An S3 object of class 'priors'

Examples

# If you believe that cases are generally reported one day after the date of
# the test, and deaths one day after the event:
cfg <- covidestim(ndays = 120, region = '09009', pop_size=get_pop('09009')) +
  priors_reporting_delays(
    cas_rep_delay = c(2.7, 3), # Mean = ~1 day
    die_rep_delay = c(2.7, 3)  # Mean = ~1 day
  )
#> Error in covidestim(ndays = 120, region = "09009", pop_size = get_pop("09009")): unused argument (ndays = 120)