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)
#> Joining with `by = join_by(date_onset)`
#> Joining with `by = join_by(date_onset, delay, Time)`
#> $total
#> # A tibble: 15 × 7
#> Time dt_event Median LI LS LIb LSb
#> <int> <date> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 17 2021-12-13 444 442 448 443 445
#> 2 18 2021-12-20 632 626 640 630 634
#> 3 19 2021-12-27 736 727 751 733 740
#> 4 20 2022-01-03 759 746 779 754 765
#> 5 21 2022-01-10 879 861 903 872 886
#> 6 22 2022-01-17 786 765 817 778 795
#> 7 23 2022-01-24 590 567 625 580 601
#> 8 24 2022-01-31 510 484 549 500 522.
#> 9 25 2022-02-07 409 378. 452. 397 422
#> 10 26 2022-02-14 403 368 455 390. 419
#> 11 27 2022-02-21 338 292 397 320 356
#> 12 28 2022-02-28 300 247. 388 280 323
#> 13 29 2022-03-07 315 243 413. 288 346
#> 14 30 2022-03-14 290 194 451. 248. 331
#> 15 31 2022-03-21 250 131. 532. 202. 316
#>