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Filter data based on availability and forecast date

Source: R/preprocess.R
filter_by_availability.Rd

Filter data based on availability and forecast date

Usage

filter_by_availability(
  obs,
  date = max(obs$date),
  seq_date = date,
  case_date = date
)

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.

date

Date at which to filter. Defaults to the maximum date in obs.

seq_date

Date from which to use available sequence data. Defaults to the date.

case_date

Date from which to use available case data. Defaults to the date.

Value

A data.frame of observations filter for the latest available data for the specified dates of interest.

See also

Preprocessing functions fv_dow_period(), latest_obs(), piecewise_steps()

Examples

options(mc.cores = 4)
obs <- filter_by_availability(
  germany_covid19_delta_obs,
  date = as.Date("2021-06-12"),
)
dt <- rbind(
  update_obs_availability(obs, seq_lag = 3),
  update_obs_availability(obs, seq_lag = 1)
)
# filter out duplicates and up to the present date
filter_by_availability(dt)
#>           date location_name location  cases cases_available seq_total seq_voc
#>  1: 2021-03-20       Germany       DE  87328      2021-03-20        NA      NA
#>  2: 2021-03-27       Germany       DE 109442      2021-03-27        NA      NA
#>  3: 2021-04-03       Germany       DE 117965      2021-04-03        NA      NA
#>  4: 2021-04-10       Germany       DE 107223      2021-04-10        NA      NA
#>  5: 2021-04-17       Germany       DE 142664      2021-04-17      4066       5
#>  6: 2021-04-24       Germany       DE 145568      2021-04-24      4494      31
#>  7: 2021-05-01       Germany       DE 131887      2021-05-01      3615      55
#>  8: 2021-05-08       Germany       DE 107141      2021-05-08      4479      86
#>  9: 2021-05-15       Germany       DE  77261      2021-05-15      3399      93
#> 10: 2021-05-22       Germany       DE  57310      2021-05-22      3275     108
#> 11: 2021-05-29       Germany       DE  33052      2021-05-29      1328      34
#> 12: 2021-06-05       Germany       DE  22631      2021-06-05        NA      NA
#> 13: 2021-06-12       Germany       DE  15553      2021-06-12        NA      NA
#>       share_voc seq_available
#>  1:          NA          <NA>
#>  2:          NA          <NA>
#>  3:          NA          <NA>
#>  4:          NA          <NA>
#>  5: 0.001229710    2021-05-08
#>  6: 0.006898086    2021-05-15
#>  7: 0.015214385    2021-05-22
#>  8: 0.019200714    2021-05-29
#>  9: 0.027360989    2021-06-05
#> 10: 0.032977099    2021-06-12
#> 11: 0.025602410    2021-06-05
#> 12:          NA    2021-06-26
#> 13:          NA    2021-07-03

# filter to only use sequence data up the the 12th of June
filter_by_availability(dt, seq_date = "2021-06-12")
#>           date location_name location  cases cases_available seq_total seq_voc
#>  1: 2021-03-20       Germany       DE  87328      2021-03-20        NA      NA
#>  2: 2021-03-27       Germany       DE 109442      2021-03-27        NA      NA
#>  3: 2021-04-03       Germany       DE 117965      2021-04-03        NA      NA
#>  4: 2021-04-10       Germany       DE 107223      2021-04-10        NA      NA
#>  5: 2021-04-17       Germany       DE 142664      2021-04-17      4066       5
#>  6: 2021-04-24       Germany       DE 145568      2021-04-24      4494      31
#>  7: 2021-05-01       Germany       DE 131887      2021-05-01      3615      55
#>  8: 2021-05-08       Germany       DE 107141      2021-05-08      4479      86
#>  9: 2021-05-15       Germany       DE  77261      2021-05-15      3399      93
#> 10: 2021-05-22       Germany       DE  57310      2021-05-22      3275     108
#> 11: 2021-05-29       Germany       DE  33052      2021-05-29      1328      34
#> 12: 2021-06-05       Germany       DE  22631      2021-06-05        NA      NA
#> 13: 2021-06-12       Germany       DE  15553      2021-06-12        NA      NA
#>       share_voc seq_available
#>  1:          NA          <NA>
#>  2:          NA          <NA>
#>  3:          NA          <NA>
#>  4:          NA          <NA>
#>  5: 0.001229710    2021-05-08
#>  6: 0.006898086    2021-05-15
#>  7: 0.015214385    2021-05-22
#>  8: 0.019200714    2021-05-29
#>  9: 0.027360989    2021-06-05
#> 10: 0.032977099    2021-06-12
#> 11: 0.025602410    2021-06-05
#> 12:          NA    2021-06-26
#> 13:          NA    2021-07-03

# as above but only use
filter_by_availability(dt,
  seq_date = "2021-06-12",
  case_date = "2021-07-01"
)
#>           date location_name location  cases cases_available seq_total seq_voc
#>  1: 2021-03-20       Germany       DE  87328      2021-03-20        NA      NA
#>  2: 2021-03-27       Germany       DE 109442      2021-03-27        NA      NA
#>  3: 2021-04-03       Germany       DE 117965      2021-04-03        NA      NA
#>  4: 2021-04-10       Germany       DE 107223      2021-04-10        NA      NA
#>  5: 2021-04-17       Germany       DE 142664      2021-04-17      4066       5
#>  6: 2021-04-24       Germany       DE 145568      2021-04-24      4494      31
#>  7: 2021-05-01       Germany       DE 131887      2021-05-01      3615      55
#>  8: 2021-05-08       Germany       DE 107141      2021-05-08      4479      86
#>  9: 2021-05-15       Germany       DE  77261      2021-05-15      3399      93
#> 10: 2021-05-22       Germany       DE  57310      2021-05-22      3275     108
#> 11: 2021-05-29       Germany       DE  33052      2021-05-29      1328      34
#> 12: 2021-06-05       Germany       DE  22631      2021-06-05        NA      NA
#> 13: 2021-06-12       Germany       DE  15553      2021-06-12        NA      NA
#>       share_voc seq_available
#>  1:          NA          <NA>
#>  2:          NA          <NA>
#>  3:          NA          <NA>
#>  4:          NA          <NA>
#>  5: 0.001229710    2021-05-08
#>  6: 0.006898086    2021-05-15
#>  7: 0.015214385    2021-05-22
#>  8: 0.019200714    2021-05-29
#>  9: 0.027360989    2021-06-05
#> 10: 0.032977099    2021-06-12
#> 11: 0.025602410    2021-06-05
#> 12:          NA    2021-06-26
#> 13:          NA    2021-07-03