man/examples/nowcast.R

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

## Basic usage of nowcast

shape_onset_to_report = 2.7
scale_onset_to_report = 1.6
delay_onset_to_report <- list(name="gamma",
                              shape = shape_onset_to_report,
                              scale = scale_onset_to_report)

corrected_incidence_data_1 <- nowcast(
  incidence_data = HK_incidence_data$onset_incidence,
  delay_until_final_report = delay_onset_to_report
)


## Advanced usage of nowcast
# Only taking into account cases that have a chance of being observed greater
# than 25%. Here, the delay between symptom onset and report is given as
# empirical delay data, hence it is needed to specify the date of the first
# entry in incidence_data

corrected_incidence_data_2 <- nowcast(
  incidence_data = HK_incidence_data$onset_incidence,
  delay_until_final_report = HK_delay_data,
  ref_date = HK_incidence_data$date[1],
  cutoff_observation_probability = 0.25
)