# Add line list event dates and case information as columns to infectious history `` These `.add_*()` functions add columns to the `` output by `.sim_network_bp()`. The `` supplied to `.data` will have a different number of columns depending on which function is being called (i.e. the `` supplied to `.add_hospitalisation()` will have more columns than the `` supplied to `.add_date_contact()` as former function is called later in the simulation). The event date could be first contact, last contact or other. ```r .add_date_contact( .data, first_contact_distribution, last_contact_distribution, outbreak_start_date ) .add_hospitalisation(.data, onset_to_hosp, hosp_risk) .add_outcome( .data, onset_to_death, onset_to_recovery, hosp_death_risk, non_hosp_death_risk, config ) .add_names(.data, anonymise = FALSE) .add_ct(.data, distribution) .add_reporting_delay(.data, reporting_delay) ``` ## Arguments - `.data`: A `` containing the infectious history from a branching process simulation (`.sim_network_bp()`). - `first_contact_distribution, last_contact_distribution`: A `function` to generate the time for the first or last contact between the infector and infectee (exposure window). See `create_config()`. - `outbreak_start_date`: A `date` for the start of the outbreak. - `onset_to_hosp`: A `function` or an `` object for the onset-to-hospitalisation delay distribution. `onset_to_hosp` can also be set to `NULL` to not simulate hospitalisation (admission) dates. The function can be defined or anonymous. The function must return a vector of `numeric`s for the length of the onset-to-hospitalisation delay. The function must have a single argument. An `` can be provided. This will be converted into a random number generator internally. The default is an anonymous function with a lognormal distribution random number generator (`rlnorm()`) with `meanlog = 1.5` and `sdlog = 0.5`. If `onset_to_hosp` is set to `NULL` then `hosp_risk` and `hosp_death_risk` will be automatically set to `NULL` if not manually specified. - `hosp_risk`: Either a single `numeric` for the hospitalisation risk of everyone in the population, or a `` with age specific hospitalisation risks. Default is 20% hospitalisation (`0.2`) for the entire population. If the `onset_to_hosp` argument is set to `NULL` this argument will automatically be set to `NULL` if not specified or can be manually set to `NULL`. See details and examples for more information. - `onset_to_death`: A `function` or an `` object for the onset-to-death delay distribution. `onset_to_death` can also be set to `NULL` to not simulate dates for individuals that died. The function can be defined or anonymous. The function must return a vector of `numeric`s for the length of the onset-to-death delay. The function must have a single argument. An `` can be provided. This will be converted into a random number generator internally. The default is an anonymous function with a lognormal distribution random number generator (`rlnorm()`) with `meanlog = 2.5` and `sdlog = 0.5`. If `onset_to_death` is set to `NULL` then `non_hosp_death_risk` and `hosp_death_risk` will be automatically set to `NULL` if not manually specified. For hospitalised cases, the function ensures the onset-to-death time is greater than the onset-to-hospitalisation time. After many (1000) attempts, if an onset-to-death time (from `onset_to_death`) cannot be sampled that is greater than a onset-to-hospitalisation time (from `onset_to_hosp`) then the function will error. Due to this conditional sampling, the onset-to-death times in the line list may not resemble the distributional form input into the function. - `onset_to_recovery`: A `function` or an `` object for the onset-to-recovery delay distribution. `onset_to_recovery` can also be `NULL` to not simulate dates for individuals that recovered. The function can be defined or anonymous. The function must return a vector of `numeric`s for the length of the onset-to-recovery delay. The function must have a single argument. An `` can be provided. This will be converted into a random number generator internally. The default is `NULL` so by default cases that recover get an `NA` in the `$date_outcome` line list column. For hospitalised cases, the function ensures the onset-to-recovery time is greater than the onset-to-hospitalisation time. After many (1000) attempts, if an onset-to-recovery time (from `onset_to_recovery`) cannot be sampled that is greater than a onset-to-hospitalisation time (from `onset_to_hosp`) then the function will error. Due to this conditional sampling, the onset-to-recovery times in the line list may not resemble the distributional form input into the function. - `hosp_death_risk`: Either a single `numeric` for the death risk for hospitalised individuals across the population, or a `` with age specific hospitalised death risks Default is 50% death risk in hospitals (`0.5`) for the entire population. If the `onset_to_death` argument is set to `NULL` this argument will automatically be set to `NULL` if not specified or can be manually set to `NULL`. See details and examples for more information. The `hosp_death_risk` can vary through time if specified in the `time_varying_death_risk` element of `config`, see `vignette("time-varying-cfr", package = "simulist")` for more information. - `non_hosp_death_risk`: Either a single `numeric` for the death risk for outside of hospitals across the population, or a `` with age specific death risks outside of hospitals. Default is 5% death risk outside of hospitals (`0.05`) for the entire population. If the `onset_to_death` argument is set to `NULL` this argument will automatically be set to `NULL` if not specified or can be manually set to `NULL`. See details and examples for more information. The `non_hosp_death_risk` can vary through time if specified in the `time_varying_death_risk` element of `config`, see `vignette("time-varying-cfr", package = "simulist")` for more information. - `config`: A list of settings to adjust the randomly sampled delays and Ct values. See `create_config()` for more information. - `anonymise`: A `logical` boolean for whether case names should be anonymised. Default is `FALSE`. - `reporting_delay`: A `function` for the reporting delay distribution or `NULL`. The (random) number generating function creates delays between the time of symptom onset (`$date_onset`) and the case being reported (`$date_reporting`). The function can be defined or anonymous. The function must return a vector of `numeric`s for the length of the reporting delay. The function must have a single argument. The default is `NULL` so by default there is no reporting delay, and the `$date_reporting` line list column is identical to the `$date_onset` column. ## Returns A `` with one more column than input into `.data`. Unless the column heading is already present in which the data is overwritten.

dot-add_cols function