Create an epidist_aggregate_data object from a data.frame

This method takes a data.frame containing event dates (primary/secondary event dates and observation date) along with counts and creates an epidist_aggregate_data object. This format is useful when working with pre-aggregated data where each row represents multiple identical observations with the count stored in a specified column. Internally it makes use of as_epidist_linelist_data.data.frame() to convert the data to a linelist format before adding the count column. See the other methods for other data input options.

Usage

# S3 method for class 'data.frame'
as_epidist_aggregate_data(
  data,
  n = NULL,
  pdate_lwr = NULL,
  sdate_lwr = NULL,
  pdate_upr = NULL,
  sdate_upr = NULL,
  obs_date = NULL,
  ...
)

Arguments

data

A data.frame containing line list data

n

A character string giving the name of the column containing the counts for each row. If NULL then the column n must be present in the data.

pdate_lwr

A string giving the column of data containing the primary event lower bound as a datetime. Defaults to NULL which assumes that the variable pdate_lwr is present.

sdate_lwr

A string giving the column of data containing the secondary event lower bound as a datetime. Defaults to NULL which assumes that the variable sdate_lwr is present.

pdate_upr

A string giving the column of data containing the primary event upper bound as a datetime. If this column exists in the data it will be used, otherwise if not supplied then the value of pdate_lwr + 1 day is used.

sdate_upr

A string giving the column of data containing the secondary event upper bound as a datetime. If this column exists in the data it will be used, otherwise if not supplied then the value of sdate_lwr + 1 day is used.

obs_date

A string giving the column of data containing the observation time as a datetime. Optional, if not supplied then the maximum of sdate_upr is used.

...

Additional arguments passed to methods

See also

Other aggregate_data: as_epidist_aggregate_data(), as_epidist_aggregate_data.default(), as_epidist_aggregate_data.epidist_linelist_data(), assert_epidist.epidist_aggregate_data(), is_epidist_aggregate_data(), new_epidist_aggregate_data()

Examples

sierra_leone_ebola_data |>
  dplyr::count(date_of_symptom_onset, date_of_sample_tested) |>
  as_epidist_aggregate_data(
    pdate_lwr = "date_of_symptom_onset",
    sdate_lwr = "date_of_sample_tested",
    n = "n"
  )
#> ℹ No primary event upper bound provided, using the primary event lower bound + 1 day as the assumed upper bound.
#> ℹ No secondary event upper bound provided, using the secondary event lower bound + 1 day as the assumed upper bound.
#> ℹ No observation time column provided, using 2015-09-14 as the observation date (the maximum of the secondary event upper bound).
#> # A tibble: 2,453 × 11
#>    ptime_lwr ptime_upr stime_lwr stime_upr obs_time pdate_lwr  sdate_lwr      n
#>        <dbl>     <dbl>     <dbl>     <dbl>    <dbl> <date>     <date>     <int>
#>  1         0         1         5         6      484 2014-05-18 2014-05-23     1
#>  2         2         3         7         8      484 2014-05-20 2014-05-25     2
#>  3         3         4         8         9      484 2014-05-21 2014-05-26     4
#>  4         4         5         9        10      484 2014-05-22 2014-05-27     6
#>  5         8         9        13        14      484 2014-05-26 2014-05-31     1
#>  6         9        10        14        15      484 2014-05-27 2014-06-01     3
#>  7        11        12        16        17      484 2014-05-29 2014-06-03     7
#>  8        12        13        17        18      484 2014-05-30 2014-06-04     7
#>  9        13        14        18        19      484 2014-05-31 2014-06-05     1
#> 10        13        14        20        21      484 2014-05-31 2014-06-07     1
#> # ℹ 2,443 more rows
#> # ℹ 3 more variables: pdate_upr <date>, sdate_upr <date>, obs_date <date>