---
title: "Using jointlyr"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Using jointlyr}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(jointlyr)
```

## Set up data

### Incidence

```{r}
incid <- c(45, 28, 91, 36, 43, 50, 77, 54, 44, 45)
```

### Serial Interval Distribution

```{r}
si_trunc <- 20
si_distr <- EpiEstim::discr_si(seq(0, si_trunc), 6.48, 3.83)
si_distr <- si_distr / sum(si_distr)
```


```{r}
## Default args for iter and chains
jointlyr::jointly_estimate(10, 100, incid, si_distr)
```