The incidence() function wraps the date grouping functionality of the grates package, providing an easy to use interface for constructing incidence objects. Sometimes, however, you may want greater flexibility in choosing how you would like to transform your “date” inputs. For this reason we also the provide the function build_incidence(), where you can specify the function you wish to apply. We illustrate this approach using both the clock and zoo packages.
library(incidence2)
library(clock)
library(zoo)
#>
#> Attaching package: 'zoo'
#> The following objects are masked from 'package:base':
#>
#> as.Date, as.Date.numeric
# data included in incidence2 but obtained via the covidregionaldata package
data("covidregionaldataUK")
dat <- covidregionaldataUKclock_month_inci <-
build_incidence(
dat,
date_index = date,
groups = region,
counts = ends_with("new"),
FUN = function(x) calendar_narrow(as_year_month_day(x), precision = "month")
)
clock_month_inci
#> An incidence object: 234 x 7
#> date range: [2020-01] to [2021-06]
#> cases_new: 8379330
#> deaths_new: 239477
#> recovered_new: 0
#> hosp_new: 466704
#> tested_new: 162328695
#>
#> date_index region cases_new deaths_new recovered_new hosp_new tested_new
#> <ymd<month>> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2020-01 East Mid… 0 0 0 0 0
#> 2 2020-01 East of … 0 0 0 0 0
#> 3 2020-01 England 2 0 0 0 0
#> 4 2020-01 London 0 0 0 0 0
#> 5 2020-01 North Ea… 0 0 0 0 0
#> 6 2020-01 North We… 0 0 0 0 0
#> 7 2020-01 Northern… 0 0 0 0 0
#> 8 2020-01 Scotland 0 0 0 0 0
#> 9 2020-01 South Ea… 0 0 0 0 0
#> 10 2020-01 South We… 0 0 0 0 0
#> # … with 224 more rowsas.yearmonzoo_month_inci <-
build_incidence(
dat,
date_index = date,
groups = region,
counts = ends_with("new"),
FUN = as.yearmon
)
zoo_month_inci
#> An incidence object: 234 x 7
#> date range: [Jan 2020] to [Jun 2021]
#> cases_new: 8379330
#> deaths_new: 239477
#> recovered_new: 0
#> hosp_new: 466704
#> tested_new: 162328695
#>
#> date_index region cases_new deaths_new recovered_new hosp_new tested_new
#> <yearmon> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Jan 2020 East Midla… 0 0 0 0 0
#> 2 Jan 2020 East of En… 0 0 0 0 0
#> 3 Jan 2020 England 2 0 0 0 0
#> 4 Jan 2020 London 0 0 0 0 0
#> 5 Jan 2020 North East 0 0 0 0 0
#> 6 Jan 2020 North West 0 0 0 0 0
#> 7 Jan 2020 Northern I… 0 0 0 0 0
#> 8 Jan 2020 Scotland 0 0 0 0 0
#> 9 Jan 2020 South East 0 0 0 0 0
#> 10 Jan 2020 South West 0 0 0 0 0
#> # … with 224 more rows# we can compare this to the grates implementation
grates_month_inci <-
incidence(
dat,
date_index = date,
groups = region,
counts = ends_with("new"),
interval = "month"
)
grates_month_inci
#> An incidence object: 234 x 7
#> date range: [2020-Jan] to [2021-Jun]
#> cases_new: 8379330
#> deaths_new: 239477
#> recovered_new: 0
#> hosp_new: 466704
#> tested_new: 162328695
#> interval: 1 month
#> cumulative: FALSE
#>
#> date_index region cases_new deaths_new recovered_new hosp_new tested_new
#> <mnth> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2020-Jan East Midla… 0 0 0 0 0
#> 2 2020-Jan East of En… 0 0 0 0 0
#> 3 2020-Jan England 2 0 0 0 0
#> 4 2020-Jan London 0 0 0 0 0
#> 5 2020-Jan North East 0 0 0 0 0
#> 6 2020-Jan North West 0 0 0 0 0
#> 7 2020-Jan Northern I… 0 0 0 0 0
#> 8 2020-Jan Scotland 0 0 0 0 0
#> 9 2020-Jan South East 0 0 0 0 0
#> 10 2020-Jan South West 0 0 0 0 0
#> # … with 224 more rows
# and check they are all "equal" ...
clock_month_inci$date_index <- as.Date(calendar_widen(clock_month_inci$date_index, "day"))
zoo_month_inci$date_index <- as.Date(zoo_month_inci$date_index)
grates_month_inci$date_index <- as.Date(grates_month_inci$date_index)
identical(
as.data.frame(clock_month_inci),
as.data.frame(zoo_month_inci)
)
#> [1] TRUE
identical(
as.data.frame(grates_month_inci),
as.data.frame(clock_month_inci)
)
#> [1] TRUE