\@description
Simulate cases from a single Rt trace, an initial number of cases, and a reporting model
This functionality has largely been superseded by `simulate_infections`

and will likely to replaced
or updated to depend on `stan`

code.

```
simulate_cases(
rts,
initial_cases,
initial_date,
generation_interval,
rdist = rpois,
delay_defs,
reporting_effect,
reporting_model,
truncate_future = TRUE,
type = "sample"
)
```

- rts
A dataframe of containing two variables

`rt`

and`date`

with`rt`

being numeric and`date`

being a date.- initial_cases
Integer, initial number of cases.

- initial_date
Date, (i.e

`as.Date("2020-02-01")`

). Starting date of the simulation.- generation_interval
Numeric vector describing the generation interval probability density

- rdist
A function to be used to sample the number of cases. Must take two arguments with the first specifying the number of samples and the second the mean. Defaults to

`rpois`

if not supplied- delay_defs
A list of single row data.tables that each defines a delay distribution (model, parameters and maximum delay for each model). See

`lognorm_dist_def`

for an example of the structure.- reporting_effect
A numeric vector of length 7 that allows the scaling of reported cases by the day on which they report (1 = Monday, 7 = Sunday). By default no scaling occurs.

- reporting_model
A function that takes a single numeric vector as an argument and returns a single numeric vector. Can be used to apply stochastic reporting effects. See the examples for details.

- truncate_future
Logical, should cases be truncated if they occur after the first date reported in the data. Defaults to

`TRUE`

.- type
Character string indicating the method to use to transform counts. Supports either "sample" which approximates sampling or "median" would shift by the median of the distribution.

A dataframe containing three variables: `date`

, `cases`

and `reference`

.

simulate_infections