nowcasting_inla: nowcasting_inla

In covid19br/nowcaster: Nowcaster

nowcasting_inla

Description

function to estimate amount of events already started by not yet notified. The main use is to estimate how many cases in a outbreak has already started their onset date of symptons but has not yet notified. nowcasting_inla, fits a statistical distribution to the empirical distribution of time of delay between onset date and report date.

Usage

nowcasting_inla(
  dataset,
  bins_age = "SI-PNI",
  trim.data = 0,
  Dmax = 15,
  wdw = 30,
  use.epiweek = FALSE,
  age_col,
  date_onset,
  date_report,
  data.by.week = FALSE,
  silent = F,
  K = 0,
  trajectories = F,
  zero_inflated = F,
  ...
)

Arguments

dataset	Dataset with at least 2 columns, date of onset, date of report. It can be a dataset with 3 columns, two dates columns as before said and a another one being an stratum column, in which data will stratified, usually being age.
bins_age	Age bins to do the nowcasting, it receive a vector of age bins, or options between, "SI-PNI", "10 years", "5 years". Default "SI-PNI".
trim.data	(in weeks) Date to be trimmed out from the data base, in days. Default 0 days.
Dmax	(in weeks) Window of dates the estimation will act, i.e., till how many past weeks the nowcasting will estimate. Default 15 weeks.
wdw	(in weeks) Until which maximum amount of weeks the Nowcasting will use to the estimation. Default 30 weeks.
use.epiweek	If TRUE, it uses the CDC epiweek definition where the week starts on Sunday, if FALSE it the week ends at the weekday of the last record date. Default FALSE
age_col	Column for ages
date_onset	Column of dates of onset of the events, normally date of onset of first symptoms of cases
date_report	Column of dates of report of the event, normally date of digitation of the notification of cases
data.by.week	If it has to be returned the whole time-series data. Default FALSE.
silent	Deprecated Should be the warnings turned off? Default is TRUE.
K	(in weeks) How much weeks to forecast ahead? Default K is 0, no forecasting ahead
trajectories	Returns the trajectories estimated on the inner 'INLA' model
zero_inflated	Experimental In non-structured models, fit a model that deals with zero-inflated data. Default FALSE. If the age_col is not missing this flag is ignored.
...	list parameters to other functions
return.age	Deprecated If the estimate by Age should be returned. Default TRUE.

Value

a list of 2 elements, each element with a data.frame with nowcasting estimation, 'Total', 'data' with the time-series out of wdw . If 'age_col' is parsed, add a thrid element with by age estimation 'age' . If 'trajectories' = TRUE, add a forth element with the returned trajectories from 'inla'.

Examples

# Loading Belo Horizonte SARI dataset
data(sragBH)
nowcasting_inla(dataset = sragBH,
                date_onset = DT_SIN_PRI,
                date_report = DT_DIGITA,
                silent = T)

covid19br/nowcaster documentation built on April 13, 2025, 6:13 a.m.