nowcasting_inla — nowcasting

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,
  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.
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)
#> Joining, by = "date_onset"
#> Joining, by = c("date_onset", "delay", "Time")
#> `summarise()` has grouped output by 'Time', 'dt_event'. You can override using
#> the `.groups` argument.
#> $total
#> # A tibble: 15 × 7
#>     Time dt_event   Median    LI    LS   LIb   LSb
#>    <int> <date>      <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1    17 2021-12-13    625  621   633   623   627 
#>  2    18 2021-12-20    695  687   708   692   699 
#>  3    19 2021-12-27    812  801   829   808.  817 
#>  4    20 2022-01-03    886  871   908   880   893 
#>  5    21 2022-01-10    818  800   846   810   826 
#>  6    22 2022-01-17    631  609   660   623   640 
#>  7    23 2022-01-24    542  517   575   532   552 
#>  8    24 2022-01-31    434  406   473   424   445 
#>  9    25 2022-02-07    422  389   465   409   434 
#> 10    26 2022-02-14    356  321   405   343   371.
#> 11    27 2022-02-21    334  291.  393.  316   351 
#> 12    28 2022-02-28    340  286   414.  321   364 
#> 13    29 2022-03-07    307  244.  402.  283   335 
#> 14    30 2022-03-14    280  190   438.  245   322 
#> 15    31 2022-03-21    229  116.  471.  181   287 
#>