pkgdown/extra.css

Skip to contents

Transform an object to count data

to_count.Rd

[Stable] Transforms a tbl.now from:

  • linelist: to count-incidence or count-cumulative

  • count-incidence: to count-cumulative

Usage

to_count(x, to = NULL, ...)

# S3 method for class 'tbl_now'
to_count(x, to = NULL, ...)

Arguments

x

Data to be transformed from linelist to count data

to

Either linelist, count-incidence or count-cumulative the resulting data-type to be created.

...

Additional arguments

Value

A tbl_now object of the requested to data type, with the counts aggregated into the case_count column.

Details

This is an S3 generic. This package provides methods for the following classes:

  • tbl_now: takes a tbl_now object and creates a new column with name n of counts of observations if data_type = "linelist".

Note

linelist data cannot be reconstructed from count-* data. Trying this will throw an error as you cannot un-count aggregated data.

Examples

data(denguedat)
ndata <- tbl_now(denguedat,
  event_date = "onset_week",
  report_date = "report_week",
  strata = "gender"
)
#> ℹ Identified data as <linelist-data> where each observation is a test.

to_count(ndata, to = "count-incidence")
#> # A tibble:  8,265 × 7
#> # Data type: "count-incidence"
#> # Frequency: Event: `weeks` | Report: `weeks`
#>    onset_week   report_week   .event_num .report_num gender         n .delay
#>    <date>       <date>             <dbl>       <dbl> <chr>      <int>  <dbl>
#>    [event_date] [report_date]      [...]       [...] [strata] [cases]  [...]
#>  1 1990-01-01   1990-01-01             0           0 Female         2      0
#>  2 1990-01-01   1990-01-08             0           1 Female        13      1
#>  3 1990-01-01   1990-01-15             0           2 Female        16      2
#>  4 1990-01-01   1990-01-22             0           3 Female         7      3
#>  5 1990-01-01   1990-03-05             0           9 Female         1      9
#>  6 1990-01-01   1990-01-01             0           0 Male           1      0
#>  7 1990-01-01   1990-01-08             0           1 Male          11      1
#>  8 1990-01-01   1990-01-15             0           2 Male           7      2
#>  9 1990-01-01   1990-01-22             0           3 Male           1      3
#> 10 1990-01-01   1990-01-29             0           4 Male           1      4
#> # ────────────────────────────────────────────────────────────────────────────────
#> # Now: 2010-12-20 | Event date: "onset_week" | Report date: "report_week"
#> # Strata: "gender"
#> # ────────────────────────────────────────────────────────────────────────────────
#> # ℹ 8,255 more rows

data("covidat")
suppressWarnings({
  ndata <- tbl_now(covidat,
    event_date = "date_of_symptom_onset",
    report_date = "date_of_registry",
    strata = "sex"
  )
  to_count(ndata)
})
#> ℹ Identified data as <linelist-data> where each observation is a test.
#> # A tibble:  40,822 × 7
#> # Data type: "linelist"
#> # Frequency: Event: `days` | Report: `days`
#>    date_of_registry date_of_symptom_onset sex          n .event_num .report_num
#>    <date>           <date>                <chr>    <int>      <dbl>       <dbl>
#>    [report_date]    [event_date]          [strata] [...]      [...]       [...]
#>  1 2020-04-05       2020-03-06            FEMALE       1          0          30
#>  2 2020-04-05       2020-03-06            MALE         1          0          30
#>  3 2020-04-05       2020-03-07            FEMALE       1          1          30
#>  4 2020-04-07       2020-03-11            MALE         1          5          32
#>  5 2020-04-05       2020-03-18            FEMALE       1         12          30
#>  6 2020-04-08       2020-03-23            FEMALE       1         17          33
#>  7 2020-04-05       2020-03-24            MALE         1         18          30
#>  8 2020-04-06       2020-03-26            FEMALE       1         20          31
#>  9 2020-04-05       2020-03-27            FEMALE       1         21          30
#> 10 2020-04-05       2020-03-31            FEMALE       1         25          30
#> # ────────────────────────────────────────────────────────────────────────────────
#> # Now: 2023-01-01 | Event date: "date_of_symptom_onset" | Report date:
#> # "date_of_registry"
#> # Strata: "sex"
#> # ────────────────────────────────────────────────────────────────────────────────
#> # ℹ 40,812 more rows
#> # ℹ 1 more variable: .delay <dbl>