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## surveil: Public health surveillance 

<img src="man/figures/logo.png" align="right" width="160" />

The *surveil* R package provides time series models for routine public health surveillance tasks: model time trends in mortality or disease incidence rates to make inferences about levels of risk, cumulative and period percent change, age-standardized rates, and health inequalities. 

*surveil* is an interface to [Stan](https://mc-stan.org), a state-of-the-art platform for Bayesian inference. For analysis of spatial health data see the [*geostan*](https://connordonegan.github.io/geostan/) R package.

### Installation

*surveil* is available on CRAN; install from R using:

```{r eval = FALSE}
install.packages("surveil")
```
### Vignettes

Review the package vignettes to get started:

 - `vignette("surveil-demo")`: An introduction to public health modeling with *surveil*
 - `vignette("age-standardization")`: How to age-standardize *surveil* model results 
 - `vignette("measuring-inequality")`: Assessing pairwise health differences with measures of inequality
 - `vignette("surveil-mcmc")`: A brief introduction to Markov chain Monte Carlo (MCMC) with *surveil*

Also see the online [documentation](https://connordonegan.github.io/surveil/reference/index.html).

### Usage

Model time series data of mortality or disease incidence by loading the *surveil* package into R together with disease surveillance data. Tables exported from CDC WONDER are automatically in the correct format.

```{r}
library(surveil)
library(knitr)
data(cancer)

kable(head(cancer), 
      booktabs = TRUE,
      caption = "Table 1. A glimpse of cancer surveillance data")
```

Model trends in risk and easily view functions of risk estimates, such as cumulative percent change:

```{r eval = FALSE}
fit <- stan_rw(data = cancer,
               time = Year, 
               group = Age)

fit_apc <- apc(fit)
plot(fit_apc, cumulative = TRUE)
```

<img src="man/figures/cpc-plot.png" align="center" width="800" />
*Cumulative percent change in US cancer incidence by age group*