incidence() works with POSIXt columns when interval = "week" but interval = "day"

[Bisaloo]

Please place an "x" in all the boxes that apply

• I have the most recent version of incidence2 and R
• I have found a bug
• I have a reproducible example

---

If a column is stored as POSIXt / datetime rather than a plain Date, incidence() will have an inconsistent behaviour and work when interval = "week" but interval = "day".

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(incidence2)

# Create a dataset with Dates stored as datetimes / POSIXt
data("covid19_england_nhscalls_2020", package = "outbreaks")

d <- covid19_england_nhscalls_2020 %>% 
  mutate(across(where(lubridate::is.Date), as.POSIXct, tz = "UTC"))

# Convert this dataset to incidence2

# WORKS
d %>%
  incidence("date",
            interval = "week",
            counts = "count"
  )
#> An incidence object: 27 x 2
#> date range: [2020-W12] to [2020-W38]
#> cases: 4101446
#> interval: 1 (Monday) week 
#> cumulative: FALSE
#> 
#>    date_index  count
#>        <yrwk>  <int>
#>  1   2020-W12 677547
#>  2   2020-W13 866757
#>  3   2020-W14 522298
#>  4   2020-W15 331617
#>  5   2020-W16 212969
#>  6   2020-W17 156984
#>  7   2020-W18 154765
#>  8   2020-W19 117314
#>  9   2020-W20 107629
#> 10   2020-W21  88949
#> # … with 17 more rows

# DOESN'T WORK
d %>%
  incidence("date",
            interval = "day",
            counts = "count"
  )
#> Error in `create_interval_string()`:
#> ! Not implemented for class POSIXct, POSIXt

#> Backtrace:
#>     ▆
#>  1. ├─d %>% incidence("date", interval = "day", counts = "count")
#>  2. └─incidence2::incidence(., "date", interval = "day", counts = "count")
#>  3.   ├─incidence2:::create_interval_string(dat$date_index)
#>  4.   └─incidence2:::create_interval_string.default(dat$date_index)
#>  5.     └─rlang::abort(...)

^{Created on 2022-11-21 with reprex v2.0.2.9000}

[TimTaylor]

Cheers - confirmed. Currently unsure if there will be a patch release with the current API though. Working on a new major release which will explicitly push date categorisation on to the user/developer in which case this approach will be defunct.

[TimTaylor]

Closed by 1ef0420

library(dplyr, warn.conflicts = FALSE)
library(incidence2)
#> Loading required package: grates
data("covid19_england_nhscalls_2020", package = "outbreaks")
covid19_england_nhscalls_2020 |> 
    mutate(across(where(lubridate::is.Date), as.POSIXct, tz = "UTC")) |> 
    incidence(date_index = "date", interval = "week", counts = "count")
#> # incidence: 27 x 3
#>    date_index count_variable  count
#>  * <isowk>    <fct>           <int>
#>  1 2020-W12   count          677547
#>  2 2020-W13   count          866757
#>  3 2020-W14   count          522298
#>  4 2020-W15   count          331617
#>  5 2020-W16   count          212969
#>  6 2020-W17   count          156984
#>  7 2020-W18   count          154765
#>  8 2020-W19   count          117314
#>  9 2020-W20   count          107629
#> 10 2020-W21   count           88949
#> # … with 17 more rows

^{Created on 2023-01-24 with reprex v2.0.2}