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+---
+output: 
+    md_document:
+        variant: gfm
+---
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  fig.path = "README_figs/README-"
+)
+```
+
+# jagsUI: Run JAGS from R
+
+<!-- badges: start -->
+[![CRAN status](https://www.r-pkg.org/badges/version/jagsUI)](https://cran.r-project.org/web/packages/jagsUI/index.html)
+[![R build status](https://github.com/kenkellner/jagsUI/workflows/R-CMD-check/badge.svg)](https://github.com/kenkellner/jagsUI/actions)
+<!-- badges: end -->
+
+This package runs `JAGS` (Just Another Gibbs Sampler) analyses from within `R`. It acts as a wrapper and alternative interface for the functions in the `rjags` package and adds some custom output and graphical options. It also makes running chains in parallel quick and easy.
+
+## Installation
+
+You can install the package from [CRAN](https://cran.r-project.org/web/packages/jagsUI/index.html), or get the development version from Github:
+
+```r
+devtools::install_github('kenkellner/jagsUI')
+```
+
+You will also need to separately install JAGS, which you can download [here](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/).
+
+## Example
+
+```{r}
+library(jagsUI)
+```
+
+Format data:
+
+```{r}
+jags_data <- list(
+  gnp = longley$GNP,
+  employed = longley$Employed,
+  n = nrow(longley)
+)
+```
+
+Write BUGS model file:
+
+```{r}
+modfile <- tempfile()
+writeLines("
+model{
+
+  # Likelihood
+  for (i in 1:n){ 
+    # Model data
+    employed[i] ~ dnorm(mu[i], tau)
+    # Calculate linear predictor
+    mu[i] <- alpha + beta*gnp[i]
+  }
+    
+  # Priors
+  alpha ~ dnorm(0, 0.00001)
+  beta ~ dnorm(0, 0.00001)
+  sigma ~ dunif(0,1000)
+  tau <- pow(sigma,-2)
+
+}
+", con=modfile)
+```
+
+Set initial values and parameters to save:
+
+```{r}
+inits <- function(){  
+  list(alpha=rnorm(1,0,1),
+       beta=rnorm(1,0,1),
+       sigma=runif(1,0,3)
+  )  
+}
+
+params <- c('alpha','beta','sigma')
+```
+
+Run JAGS:
+
+```{r}
+out <- jags(data = jags_data,
+            inits = inits,
+            parameters.to.save = params,
+            model.file = modfile,
+            n.chains = 3,
+            n.adapt = 100,
+            n.iter = 1000,
+            n.burnin = 500,
+            n.thin = 2)
+```
+
+View output:
+
+```{r}
+out
+```
+
+## Acknowledgments
+
+* Martyn Plummer, developer of the excellent JAGS software package and the `rjags` R package.
+* Andrew Gelman, Sibylle Sturtz, Uwe Ligges, Yu-Sung Su, and Masanao Yajima, developers of the `R2WinBUGS` and `R2jags` packages on which the package was originally based.
+* Robert Swihart, Marc Kery, Jerome Guelat, Michael Schaub, and Mike Meredith who tested and provided helpful suggestions and improvements for the package.