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nowcasting_mgcv

Source: R/nowcasting_mgcv.R
nowcasting_mgcv.Rd

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_mgcv, fits a statistical distribution to the empirical distribution of time of delay between onset date and report date.

Usage

nowcasting_mgcv(
  dataset,
  bins_age = "SI-PNI",
  trim.data = 0,
  Dmax = 15,
  wdw = 30,
  use.epiweek = TRUE,
  age_col,
  date_onset,
  date_report,
  data.by.week = FALSE,
  return.age = NULL,
  silent = FALSE,
  method.group.gam = "fs",
  K = 0,
  trajectories = FALSE,
  ...
)

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". The default is "SI-PNI".

trim.data

(in weeks) Date to be trimmed out from the data base, in days. Default is 0 days.

Dmax

(in weeks) Window of dates the estimation will act, i.e., till how many past weeks the nowcasting will estimate. Default is 15 weeks.

wdw

(in weeks) Until which maximum amount of weeks the Nowcasting will use to the estimation. Default is 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 is TRUE

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 is FALSE.

return.age

Deprecated. If the estimate by Age should be returned. Default is TRUE.

silent

Deprecated. Should be the warnings turned off? . The default is FALSE

method.group.gam

Method for aggregated smooth function in gam. Default is "fs" factor smooth, another alternative is "by".

K

(in weeks) How much weeks to forecast ahead? . The default is K = 0, no forecasting ahead

trajectories

Returns the predictive trajectories. The default is FALSE.

...

list parameters to other functions

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 third element with by age estimation 'age' . If 'trajectories' = TRUE, add a forth element with the returned trajectories from 'inla'.

Examples

# \donttest{
# Loading Belo Horizonte SARI dataset
data(sragBH)
output <- nowcasting_mgcv(dataset = sragBH,
                date_onset = DT_SIN_PRI,
                date_report = DT_DIGITA)
#> Nowcasting only
#> Warning: Using default to maximum delay, 'Dmax = 15'
#> Warning: Using default to window of action, 'wdw = 30'
#> Warning: Using default to returning option for the data, 'data.by.week = FALSE'
#> Warning: Not returning trajectories
#> Warning: 'age_col' missing, nowcasting with unstructured model
#> Warning: Using default, trimming out 0 days of data
#> Joining with `by = join_by(date_onset)`
#> Joining with `by = join_by(date_onset, delay, Time)`
# }