Create an epidist_linelist_data object from a data frame with event dates

This method takes a data.frame containing event dates (primary/secondary event dates and observation date) and creates an epidist_linelist_data object. This format is useful when working with individual-level data where each row represents a single observation. Internally it converts dates to numeric times relative to the earliest primary event date and uses as_epidist_linelist_data.default() to create the final object. See the other methods for other data input options.

Usage

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

Arguments

data

A data.frame containing line list 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 linelist_data: as_epidist_linelist_data(), as_epidist_linelist_data.default(), as_epidist_linelist_data.epidist_aggregate_data(), assert_epidist.epidist_linelist_data(), is_epidist_linelist_data(), new_epidist_linelist_data()

Examples

sierra_leone_ebola_data |>
  as_epidist_linelist_data(
    pdate_lwr = "date_of_symptom_onset",
    sdate_lwr = "date_of_sample_tested"
  )
#> 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: 8,358 × 15
#>    ptime_lwr ptime_upr stime_lwr stime_upr obs_time    id   age sex   pdate_lwr 
#>        <dbl>     <dbl>     <dbl>     <dbl>    <dbl> <int> <dbl> <chr> <date>    
#>  1         0         1         5         6      484     1    20 Fema… 2014-05-18
#>  2         2         3         7         8      484     2    42 Fema… 2014-05-20
#>  3         2         3         7         8      484     3    45 Fema… 2014-05-20
#>  4         3         4         8         9      484     4    15 Fema… 2014-05-21
#>  5         3         4         8         9      484     5    19 Fema… 2014-05-21
#>  6         3         4         8         9      484     6    55 Fema… 2014-05-21
#>  7         3         4         8         9      484     7    50 Fema… 2014-05-21
#>  8         4         5         9        10      484     8     8 Fema… 2014-05-22
#>  9         4         5         9        10      484     9    54 Fema… 2014-05-22
#> 10         4         5         9        10      484    10    57 Fema… 2014-05-22
#> # ℹ 8,348 more rows
#> # ℹ 6 more variables: sdate_lwr <date>, district <chr>, chiefdom <chr>,
#> #   pdate_upr <date>, sdate_upr <date>, obs_date <date>