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update README to include quick start using defaults, relates #120
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joshwlambert committed Jun 25, 2024
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Expand Up @@ -57,10 +57,21 @@ pak::pak("epiverse-trace/simulist")

```{r load-simulist}
library(simulist)
library(epiparameter)
```

The line list simulation requires that we define a contact distribution, period of infectiousness, onset-to-hospitalisation delay, and onset-to-death delay. We can load these from the library of epidemiological parameters in the `{epiparameter}` R package if available, or if these are not in the database yet (such as the contact distribution for COVID-19) we can define them ourselves.
A line list can be simulated by calling `sim_linelist()`. The function provides sensible defaults to quickly generate a epidemiologically valid data set.

```{r, sim-linelist-defaults}
set.seed(1)
linelist <- sim_linelist()
head(linelist)
```

However, to simulate a more realistic line list using epidemiological parameters estimated for a infectious disease we can use previously estimated epidemiological parameters. These can be from the `{epiparameter}` R package if available, or if these are not in the `{epiparameter}` database yet (such as the contact distribution for COVID-19) we can define them ourselves. Here we define a contact distribution, period of infectiousness, onset-to-hospitalisation delay, and onset-to-death delay.

```{r load-epiparameter}
library(epiparameter)
```

```{r create-epidists}
# create COVID-19 contact distribution
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