Detection of accumulation for forecasts doesn't work

[sbfnk]

I can see where the issue is and will try to issue a fix

library("EpiNow2")
#> 
#> Attaching package: 'EpiNow2'
#> The following object is masked from 'package:stats':
#> 
#>     Gamma
library("data.table")

reported_cases <- EpiNow2::example_confirmed
reported_cases_weekly <- data.table::copy(reported_cases)
reported_cases_weekly[, confirm := frollsum(confirm, 7)]
reported_cases_weekly <- fill_missing(
  reported_cases_weekly[seq(7, nrow(reported_cases_weekly), 7)],
  missing_dates = "accumulate"
)
#> Warning: ! Initial data point not marked as accumulated but some others are.
#> ℹ This means that the first data point will not be included in the likelihood.
#> ℹ To change this behaviour, set `initial_accumulate` (including setting it to 1
#>   if the first data point is to be taken as is, i.e. as the first daily data
#>   point).

est <- epinow(
  reported_cases_weekly,
  generation_time = generation_time_opts(example_generation_time),
  verbose = FALSE
)
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2 logs to the console and:
#> '/var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpuWHsSK/regional-epinow/2020-06-26.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to the console and:
#> '/var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpuWHsSK/epinow/2020-06-26.log'.
#> WARN [2025-01-28 14:08:35] epinow: The `filter_leading_zeros` argument of `estimate_infections()` is deprecated as of EpiNow2 1.7.0. - 
#> WARN [2025-01-28 14:08:35] epinow: The `zero_threshold` argument of `estimate_infections()` is deprecated as of EpiNow2 1.7.0. -
#> ℹ As of version 1.5.0 missing dates or dates with `NA` cases are treated as
#>   missing. This is in contrast to previous versions where these were
#>   interpreted as dates with zero cases.
#> ℹ In order to treat missing or `NA` cases as zeroes, see solutions in
#>   <https://github.com/epiforecasts/EpiNow2/issues/767#issuecomment-2348805272>
#> ℹ If the data is reported at non-daily intervals (for example weekly), consider
#>   using `obs_opts(na="accumulate")`.
#> ℹ For more information on these options, see `?obs_opts`.
#> This message is displayed once every 8 hours.
#> WARN [2025-01-28 14:12:04] epinow: There were 22 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. - 
#> WARN [2025-01-28 14:12:04] epinow: Examine the pairs() plot to diagnose sampling problems
#>  - 
#> WARN [2025-01-28 14:12:05] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#bulk-ess -

est$estimates$summarised[variable == "reported_cases", list(date, type)]
#>           date                           type
#>         <Date>                         <char>
#>  1: 2020-03-06                       estimate
#>  2: 2020-03-13                       estimate
#>  3: 2020-03-20                       estimate
#>  4: 2020-03-27                       estimate
#>  5: 2020-04-03                       estimate
#>  6: 2020-04-10                       estimate
#>  7: 2020-04-17                       estimate
#>  8: 2020-04-24                       estimate
#>  9: 2020-05-01                       estimate
#> 10: 2020-05-08                       estimate
#> 11: 2020-05-15                       estimate
#> 12: 2020-05-22                       estimate
#> 13: 2020-05-29                       estimate
#> 14: 2020-06-05                       estimate
#> 15: 2020-06-12                       estimate
#> 16: 2020-06-19 estimate based on partial data
#> 17: 2020-06-26 estimate based on partial data
#> 18: 2020-06-27                       forecast
#> 19: 2020-06-28                       forecast
#> 20: 2020-06-29                       forecast
#> 21: 2020-06-30                       forecast
#> 22: 2020-07-01                       forecast
#> 23: 2020-07-02                       forecast
#> 24: 2020-07-03                       forecast
#>           date                           type

^{Created on 2025-01-28 with reprex v2.1.1}