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Update observations based on availability

Source: R/data-scenarios.R
update_obs_availability.Rd

Update observations based on availability

Usage

update_obs_availability(obs, cases_lag, seq_lag)

Arguments

obs

A data.frame with the following variables: date, cases, seq_voc, and seq_total, cases_available, and seq_available. seq_available and case_available must be uniquely define data rows but other rows can be duplicated based on data availability. This data format allows for multiple versions of case and sequence data for a given date with different reporting dates. This is important when using the package in evaluation settings or in real-time where data sources are liable to be updated as new data becomes available. See germany_covid19_delta_obs for an example of a supported data set.

cases_lag

Number of weeks that case data takes to be reported. Defaults to not alter the input data.

seq_lag

Number of weeks that sequence data takes to be reported. Defaults to not alter the input data.

Value

A data.frame of observations with updated case and sequence availability dates.

See also

Functions to define and create data scenarios define_scenarios(), generate_obs_scenario()

Examples

update_obs_availability(
  germany_covid19_delta_obs,
  cases_lag = 2, seq_lag = 3
)
#>            date location_name location  cases cases_available seq_total seq_voc
#>   1: 2021-03-20       Germany       DE  87328      2021-04-03        NA      NA
#>   2: 2021-03-27       Germany       DE 109442      2021-04-10        NA      NA
#>   3: 2021-04-03       Germany       DE 117965      2021-04-17        NA      NA
#>   4: 2021-04-10       Germany       DE 107223      2021-04-24        NA      NA
#>   5: 2021-04-17       Germany       DE 142664      2021-05-01      3757       3
#>  ---                                                                           
#> 110: 2021-08-14       Germany       DE  28646      2021-08-28        NA      NA
#> 111: 2021-08-21       Germany       DE  44862      2021-09-04        NA      NA
#> 112: 2021-08-28       Germany       DE  62984      2021-09-11        NA      NA
#> 113: 2021-09-04       Germany       DE  71057      2021-09-18        NA      NA
#> 114: 2021-09-11       Germany       DE  75107      2021-09-25        NA      NA
#>         share_voc seq_available
#>   1:           NA          <NA>
#>   2:           NA          <NA>
#>   3:           NA          <NA>
#>   4:           NA          <NA>
#>   5: 0.0007985094    2021-05-08
#>  ---                           
#> 110:           NA          <NA>
#> 111:           NA          <NA>
#> 112:           NA          <NA>
#> 113:           NA          <NA>
#> 114:           NA          <NA>