Nowcast Cases by Specimen Collection Date — nowcast

nowcast_cases() predicts the number of cases expected through the current date given a linelist of cases with collection and report dates. It uses estimate_delay() to determine the last complete collection date and forecasts from that point. Cases are predicted by a weighted ensemble of two log-linear structural time series models with semilocal and robust (Student-t) trends.

nowcast_cases(
  .data,
  .collection_date = "collection_date",
  .report_date = "report_date",
  today = Sys.Date(),
  iterations = ceiling(10000/(1 - burn)),
  burn = 0.2
)

Arguments

.data: A linelist of incident cases/tests as a data frame
.collection_date: A Date column containing the test date
.report_date: A Date column containing the report date
today: The date to consider "today"
iterations: The number of MCMC iterations for each model in the ensemble; the total number of iterations will be twice this amount.
burn: The percentage of initial iterations to discard for each model