---
title: "ZooRisk: Quantitative Assessment of Zoonotic Disease Risk"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{ZooRisk: Quantitative Assessment of Zoonotic Disease Risk}
  %\VignetteEngine{knitr::rmarkdown}
---

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

## Overview

ZooRisk provides transparent quantitative tools for zoonotic disease risk,
including exposure, transmission, spillover, One Health comparison,
transmission-network analysis, uncertainty simulation, and sensitivity analysis.

## Risk assessment

```{r}
risk <- zoonotic_risk(.20, .35, .10, .60)
risk
summary(risk)
```

## Simulation

```{r}
sim <- risk_simulate(
  prevalence = c(.10, .30),
  exposure = c(.20, .50),
  transmission = c(.02, .10),
  susceptibility = c(.40, .80),
  n_sim = 1000,
  seed = 42
)
monte_carlo_risk(sim)
```

## Transmission network

```{r}
net <- transmission_network(
  from = c("cattle", "cattle", "dog"),
  to = c("dog", "human", "human")
)
network_risk(net)
```