Calculate cumulative reported cases from incidence of new reports

Calculate cumulative reported cases from incidence of new reports

Usage

enw_add_cumulative(obs, by = NULL, copy = TRUE)

Arguments

obs

A data.frame containing at least the following variables: reference date (index date of interest), report_date (report date for observations), and new_confirm (incident observations by reference and report date).

by

A character vector describing the stratification of observations. This defaults to no grouping. This should be used when modelling multiple time series in order to identify them for downstream modelling

copy

Should obs be copied (default) or modified in place?

Value

The input data.frame with a new variable confirm.

See also

Data converters enw_add_incidence(), enw_aggregate_cumulative(), enw_cumulative_to_incidence(), enw_incidence_to_cumulative(), enw_incidence_to_linelist(), enw_linelist_to_incidence()

Examples

# Default reconstruct incidence
dt <- germany_covid19_hosp[location == "DE"][age_group == "00+"]
dt <- enw_add_incidence(dt)
dt <- dt[, confirm := NULL]
enw_add_cumulative(dt)
#> Key: <reference_date, report_date>
#>        reference_date location age_group report_date new_confirm delay confirm
#>                <IDat>   <fctr>    <fctr>      <IDat>       <int> <int>   <int>
#>     1:     2021-04-06       DE       00+  2021-04-06         149     0     149
#>     2:     2021-04-06       DE       00+  2021-04-07         140     1     289
#>     3:     2021-04-06       DE       00+  2021-04-08          61     2     350
#>     4:     2021-04-06       DE       00+  2021-04-09          52     3     402
#>     5:     2021-04-06       DE       00+  2021-04-10          36     4     438
#>    ---                                                                        
#> 12911:     2021-10-18       DE       00+  2021-10-19          70     1     113
#> 12912:     2021-10-18       DE       00+  2021-10-20          29     2     142
#> 12913:     2021-10-19       DE       00+  2021-10-19         223     0     223
#> 12914:     2021-10-19       DE       00+  2021-10-20         164     1     387
#> 12915:     2021-10-20       DE       00+  2021-10-20         235     0     235

# Make use of maximum reported to calculate empirical daily reporting
enw_add_cumulative(dt)
#> Key: <reference_date, report_date>
#>        reference_date location age_group report_date new_confirm delay confirm
#>                <IDat>   <fctr>    <fctr>      <IDat>       <int> <int>   <int>
#>     1:     2021-04-06       DE       00+  2021-04-06         149     0     149
#>     2:     2021-04-06       DE       00+  2021-04-07         140     1     289
#>     3:     2021-04-06       DE       00+  2021-04-08          61     2     350
#>     4:     2021-04-06       DE       00+  2021-04-09          52     3     402
#>     5:     2021-04-06       DE       00+  2021-04-10          36     4     438
#>    ---                                                                        
#> 12911:     2021-10-18       DE       00+  2021-10-19          70     1     113
#> 12912:     2021-10-18       DE       00+  2021-10-20          29     2     142
#> 12913:     2021-10-19       DE       00+  2021-10-19         223     0     223
#> 12914:     2021-10-19       DE       00+  2021-10-20         164     1     387
#> 12915:     2021-10-20       DE       00+  2021-10-20         235     0     235