add argument to configure a incubation time

[avallecam]

Currently, the date of infection is equal to the date of symptoms onset.

epidemic curves can be used to infer the probable date of exposure (if known incubation period), or calculate the incubation period (if data of exposure is known). Including the incubation period in the configuration could help use {simulist} for outbreak investigation of point source or extended source epidemics

simulist/R/sim_internal.R

Line 59 in c9e5696

.data$date_onset <- .data$time + outbreak_start_date

[joshwlambert]

Thanks for the suggestion @avallecam! I agree that including the incubation period could be useful and I'm open to adding it to the package. A couple of questions that will help my thinking:

1. Do you think the incubation_period argument should be in the function signature of sim_linelist(), or in the config list? On initial thought, it seems to me it should go in the main function signature along with the other delay distributions (onset-to-hospitalisation onset-to-death, etc.), but I'd be interested to hear your thoughts.
2. What are the main use cases for this addition? Are there analyses or tutorials that will use this new functionality?

[joshwlambert]

This feature is added in PR #275. Getting input on the two questions above would still be useful.