Fix plot.estimate_secondary() for forecast_secondary() output

[jamesmbaazam]

Description

This PR closes #702 by reverting a change that removed NA secondary rows, thereby dropping the data needed to plot forecast "secondary" outcomes.

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
• I have added or updated unit tests where necessary.
• I have updated the documentation if required and rebuilt docs if yes (using devtools::document()).
• I have followed the established coding standards (and checked using lintr::lint_package()).
• I have added a news item linked to this PR.

After the initial Pull Request

• I have reviewed Checks for this PR and addressed any issues as far as I am able.

[jamesmbaazam]

New plot with code in linked issue

devtools::load_all()
library(cfr)
library(tidyverse)

# data --------------------------------------------------------------------

reported_cases_deaths <- cfr::ebola1976 %>% 
  dplyr::rename(primary = cases, secondary = deaths)

# Estimate from day 1 to day 35 of this data
cases_to_estimate <- reported_cases_deaths %>%
  slice(1:35)

# Forecast from day 36 to day 73
cases_to_forecast <- reported_cases_deaths %>%
  dplyr::slice(36:73) %>% 
  dplyr::mutate(value = primary)


# EpiNow2 -----------------------------------------------------------------

# delay
delay_uncertain <- EpiNow2::Gamma(
  mean = EpiNow2::Normal(mean = 14, sd = 0.5),
  sd = EpiNow2::Normal(mean = 5, sd = 0.5),
  max = 30
)

# estimate secondary cases
secondary_uncertain <- EpiNow2::estimate_secondary(
  data = cases_to_estimate,
  delays = EpiNow2::delay_opts(delay_uncertain)
)

# forecast secondary cases
forecast_uncertain <- EpiNow2::forecast_secondary(
  estimate = secondary_uncertain,
  primary = cases_to_forecast
)

plot(forecast_uncertain)

[seabbs]

Nice. LGTM