Report case counts by date of report

Convolves latent infections to reported cases via an observation model. Likely to be removed/replaced in later releases by functionality drawing on the stan implementation.

Usage

report_cases(
  case_estimates,
  case_forecast = NULL,
  delays,
  type = "sample",
  reporting_effect,
  CrIs = c(0.2, 0.5, 0.9)
)

Arguments

case_estimates

A data.table of case estimates with the following variables: date, sample, cases

case_forecast

A data.table of case forecasts with the following variables: date, sample, cases. If not supplied the default is not to incorporate forecasts.

delays

A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts() and the examples below for details.

type

Character string indicating the method to use to transform counts. Supports either "sample" which approximates sampling or "median" would shift by the median of the distribution.

reporting_effect

A data.table giving the weekly reporting effect with the following variables: sample (must be the same as in nowcast), effect (numeric scaling factor for each weekday),day (numeric 1 - 7 (1 = Monday and 7 = Sunday)). If not supplied then no weekly reporting effect is assumed.

CrIs

Numeric vector of credible intervals to calculate.

Value

A list of data.tables. The first entry contains the following variables sample, date and cases with the second being summarised across samples.

Examples

# \donttest{
# This function is deprecated and its functionality can now be accessed
# from [simulate_secondary()].
# Here are some examples of how to use [simulate_secondary()] to replace
# report_cases().
# Old (using report_cases()):
# Define case data
cases <- example_confirmed[1:40]
cases <- cases[, cases := as.integer(confirm)]
cases <- cases[, confirm := NULL][, sample := 1]
reported_cases <- report_cases(
 case_estimates = cases,
 delays = delay_opts(example_incubation_period + example_reporting_delay),
 type = "sample"
)
#> Warning: `report_cases()` was deprecated in EpiNow2 1.5.0.
#> ℹ Please use `simulate_secondary()` instead.
#> ℹ See equivalent examples using `simulate_secondary()`
#> ℹ in ?report_cases.
#> ℹ This function will be removed completely in version 2.0.0.
print(reported_cases$samples)
#>     sample       date value
#>      <int>     <Date> <int>
#>  1:      1 2020-02-25     1
#>  2:      1 2020-02-26     3
#>  3:      1 2020-02-27    14
#>  4:      1 2020-02-28    19
#>  5:      1 2020-02-29    29
#>  6:      1 2020-03-01    40
#>  7:      1 2020-03-02    65
#>  8:      1 2020-03-03    82
#>  9:      1 2020-03-04   112
#> 10:      1 2020-03-05   155
#> 11:      1 2020-03-06   195
#> 12:      1 2020-03-07   242
#> 13:      1 2020-03-08   303
#> 14:      1 2020-03-09   367
#> 15:      1 2020-03-10   462
#> 16:      1 2020-03-11   525
#> 17:      1 2020-03-12   635
#> 18:      1 2020-03-13   824
#> 19:      1 2020-03-14   957
#> 20:      1 2020-03-15  1172
#> 21:      1 2020-03-16  1350
#> 22:      1 2020-03-17  1489
#> 23:      1 2020-03-18  1783
#> 24:      1 2020-03-19  2121
#> 25:      1 2020-03-20  2362
#> 26:      1 2020-03-21  2787
#> 27:      1 2020-03-22  2985
#> 28:      1 2020-03-23  3261
#> 29:      1 2020-03-24  3582
#> 30:      1 2020-03-25  3994
#> 31:      1 2020-03-26  4485
#> 32:      1 2020-03-27  4816
#> 33:      1 2020-03-28  5077
#> 34:      1 2020-03-29  5196
#> 35:      1 2020-03-30  5284
#> 36:      1 2020-03-31  5329
#> 37:      1 2020-04-01  5483
#>     sample       date value

# New (using simulate_secondary()):
cases <- example_confirmed[1:40]
cases <- cases[, primary := as.integer(confirm)]
report <- simulate_secondary(
 cases,
 delays = delay_opts(
   fix_dist(example_incubation_period + example_reporting_delay)
 ),
 obs = obs_opts(family = "poisson")
)
print(report)
#>      date.date secondary
#>         <Date>     <num>
#>  1: 2020-02-22         0
#>  2: 2020-02-23         0
#>  3: 2020-02-24         0
#>  4: 2020-02-25         1
#>  5: 2020-02-26         5
#>  6: 2020-02-27         6
#>  7: 2020-02-28        16
#>  8: 2020-02-29        26
#>  9: 2020-03-01        30
#> 10: 2020-03-02        49
#> 11: 2020-03-03        64
#> 12: 2020-03-04       115
#> 13: 2020-03-05       137
#> 14: 2020-03-06       168
#> 15: 2020-03-07       242
#> 16: 2020-03-08       307
#> 17: 2020-03-09       372
#> 18: 2020-03-10       403
#> 19: 2020-03-11       539
#> 20: 2020-03-12       585
#> 21: 2020-03-13       793
#> 22: 2020-03-14       964
#> 23: 2020-03-15      1114
#> 24: 2020-03-16      1304
#> 25: 2020-03-17      1450
#> 26: 2020-03-18      1725
#> 27: 2020-03-19      2085
#> 28: 2020-03-20      2290
#> 29: 2020-03-21      2607
#> 30: 2020-03-22      2855
#> 31: 2020-03-23      3288
#> 32: 2020-03-24      3517
#> 33: 2020-03-25      3953
#> 34: 2020-03-26      4407
#> 35: 2020-03-27      4727
#> 36: 2020-03-28      5113
#> 37: 2020-03-29      5173
#> 38: 2020-03-30      5269
#> 39: 2020-03-31      5322
#> 40: 2020-04-01      5558
#>      date.date secondary
# }