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add missing epiweeks from reporting-delay-truncation vignette
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joshwlambert committed Feb 7, 2025
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Expand Up @@ -357,7 +357,7 @@ weekly_inci <- incidence(
plot(weekly_inci)
```

By looking at the outbreak, we can pick three points to truncate: 1) early in the outbreak when the epicurve is growing (1st February 2023, epiweek ?), 2) in the middle of the outbreak (15th March 2023, epiweek ?), and 3) late in the outbreak when the number of cases is declining and the end of the outbreak is near (1st May 2023, epiweek ?).
By looking at the outbreak, we can pick three points to truncate: 1) early in the outbreak when the epicurve is growing (1st February 2023, epiweek 5), 2) in the middle of the outbreak (15th March 2023, epiweek 11), and 3) late in the outbreak when the number of cases is declining and the end of the outbreak is near (1st May 2023, epiweek 18).

We use the `max_date` argument in `truncation()` to specify the date we want to apply the right-truncation to, i.e. the sample truncation times are applied to `max_date` and not the day the outbreak is considered over (day of last event, the default setting). For this example we will set the right-truncation delay distribution to zero so it does not remove any cases before the `max_date`, and use the default truncation event (reporting date).

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