Allow count to work on multiple columns at once

[TimTaylor]

Count should be made to work on multiple columns at once.

[TimTaylor]

Experimenting in https://github.com/reconhub/incidence2/tree/counting branch. @thibautjombart New behaviour

library(incidence2)
library(magrittr)

url <- "https://api.coronavirus.data.gov.uk/v2/data?areaType=nation&metric=newAdmissions&metric=newCasesBySpecimenDate&format=csv"
dat <- read.csv(url)

res <- 
  dat %>% 
  incidence(
    date_index = date, 
    groups = areaName, 
    counts = c(newCasesBySpecimenDate, newAdmissions)
  )

# res now has two count columns
res
#> An incidence2 object: 1,475 x 4
#> 4071183 newCasesBySpecimenDate from days 2020-01-30 to 2021-02-16
#> 427866 newAdmissions from days 2020-01-30 to 2021-02-16
#> interval: 1 day
#> cumulative: FALSE
#> 
#>    date_index areaName         newCasesBySpecimenDate newAdmissions
#>    <date>     <chr>                             <int>         <int>
#>  1 2020-01-30 England                               2             0
#>  2 2020-01-31 England                               0             0
#>  3 2020-02-01 England                               0             0
#>  4 2020-02-02 England                               0             0
#>  5 2020-02-03 England                               0             0
#>  6 2020-02-03 Northern Ireland                      0             0
#>  7 2020-02-04 England                               0             0
#>  8 2020-02-04 Northern Ireland                      0             0
#>  9 2020-02-05 England                               1             0
#> 10 2020-02-05 Northern Ireland                      0             0
#> # … with 1,465 more rows

get_count_names(res)
#> [1] "newCasesBySpecimenDate" "newAdmissions"

# subsetting columns maintains incidence class as long as atleast one count
# column remains present

res[-4]   # maintains class
#> An incidence2 object: 1,475 x 3
#> 4071183 newCasesBySpecimenDate from days 2020-01-30 to 2021-02-16
#> interval: 1 day
#> cumulative: FALSE
#> 
#>    date_index areaName         newCasesBySpecimenDate
#>    <date>     <chr>                             <int>
#>  1 2020-01-30 England                               2
#>  2 2020-01-31 England                               0
#>  3 2020-02-01 England                               0
#>  4 2020-02-02 England                               0
#>  5 2020-02-03 England                               0
#>  6 2020-02-03 Northern Ireland                      0
#>  7 2020-02-04 England                               0
#>  8 2020-02-04 Northern Ireland                      0
#>  9 2020-02-05 England                               1
#> 10 2020-02-05 Northern Ireland                      0
#> # … with 1,465 more rows

res[-3]   # maintains class
#> An incidence2 object: 1,475 x 3
#> 427866 newAdmissions from days 2020-01-30 to 2021-02-16
#> interval: 1 day
#> cumulative: FALSE
#> 
#>    date_index areaName         newAdmissions
#>    <date>     <chr>                    <int>
#>  1 2020-01-30 England                      0
#>  2 2020-01-31 England                      0
#>  3 2020-02-01 England                      0
#>  4 2020-02-02 England                      0
#>  5 2020-02-03 England                      0
#>  6 2020-02-03 Northern Ireland             0
#>  7 2020-02-04 England                      0
#>  8 2020-02-04 Northern Ireland             0
#>  9 2020-02-05 England                      0
#> 10 2020-02-05 Northern Ireland             0
#> # … with 1,465 more rows

res[1:2]  # drops class
#> # A tibble: 1,475 x 2
#>    date_index areaName        
#>    <date>     <chr>           
#>  1 2020-01-30 England         
#>  2 2020-01-31 England         
#>  3 2020-02-01 England         
#>  4 2020-02-02 England         
#>  5 2020-02-03 England         
#>  6 2020-02-03 Northern Ireland
#>  7 2020-02-04 England         
#>  8 2020-02-04 Northern Ireland
#>  9 2020-02-05 England         
#> 10 2020-02-05 Northern Ireland
#> # … with 1,465 more rows

# plot will default to first value in get_count_names(res)

res %>% plot()

res %>% plot(count = "newAdmissions")

^{Created on 2021-02-18 by the reprex package (v1.0.0)}