improve handling of seeding time in simulate_infections()

[sbfnk]

Description

This PR closes #626.

It adds a seeding_time argument, adjusts the initial number of infections, and improves the documentation.

Using the example from the linked issue now yields:

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

R <- data.frame(
  date = seq.Date(as.Date("2023-01-01"), length.out = 5, by = "day"),
  R = c(rep(1.2, 5))
)

sim <- simulate_infections(
  R = R,
  initial_infections = 100,
  generation_time = generation_time_opts(
    fix_dist(example_generation_time)
  ),
  delays = delay_opts(fix_dist(example_reporting_delay)),
  obs = obs_opts(family = "poisson")
)

sim[variable == "infections"]
#>      variable       date    value
#>        <char>     <Date>    <num>
#> 1: infections 2023-01-01 103.7012
#> 2: infections 2023-01-02 109.0943
#> 3: infections 2023-01-03 114.6880
#> 4: infections 2023-01-04 120.5479
#> 5: infections 2023-01-05 126.6988

^{Created on 2024-03-26 with reprex v2.1.0}

It starts with 100 infections as expected and the first data point shown is the number of infections occurring on the following day.

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.

[sbfnk]

windows test currently no longer failing due to what looks like an unrelated issue

[jamesmbaazam]

Sorry, I'm yet to review the part when seeding_time is applied. I'm in a workshop today so have limited capacity.

[jamesmbaazam]

LGTM.

[jamesmbaazam]

Oopsie! I was reviewing it at the same time as you were merging.

[sbfnk]

Oopsie! I was reviewing it at the same time as you were merging.

That was the merge queue automatically merging as soon as you approved.

[jamesmbaazam]

Oh, cool! It happened so fast, I thought there was a clash.