Allow reporting delay to be applied to different date events

[joshwlambert]

Currently the $date_reporting column is the date of symptom onset plus any user-specified reporting delay distribution. Given in real outbreak scenarios that the reporting date can be after symptom onset, hospital admission or outcome it would be useful to allow the user to adjust what the reporting delay is added to.

This can be added as a option in config, e.g. config$reporting_trigger = "onset", but could alternatively accept "admission" or "outcome".

[joshwlambert]

Pushing this feature to v0.6.0 because the package is now ready for a new release to get the new functionality (incl. messy_linelist() and truncate_linelist()) and bug fixes on CRAN and available to all users.

[joshwlambert]

Removing this from v0.6.0 milestone and from immediate development because it is not clear how to handle cases where the date of hospital admission or outcome is the event that triggers reporting, but the case does not have an admission date (i.e. did not get hospitalised) or an outcome date (by default recoveries don't have an outcome date).

One option is to fall back to the latest date that is given for each case, e.g. if date of admission is the data entry event, but only the symptom onset date for that case is available then use this as the reporting date. However, this may cause confusion if there is a mix of triggers for the reporting date.

Work-in-progress on this feature on the ll-input-event branch.