---
title: "How to prepare"
author: "Peter Solymos and Subhash Lele"
output: pdf_document
layout: course
course:
  location: Madison
  year: 2016
  title: "Hierarchical Models Made Easy — July 16, 2016 — Madison, WI — NACCB Congress"
  lecture: How to prepare
  file: how-to-prepare
  previous: index
  next: Hierarchical-Models-Made-Easy_Intro
  pdf: Hierarchical-Models-Made-Easy_Intro.pdf
---

Please follow these steps and install necessary software onto your computer that you are going to use at the course. This way we can spend more time on talking about modeling.

## Install R

Follow the instructions at the [R website](http://cran.r-project.org) to download and install
the most up-to-date base R version suitable for your operating system (the latest R version at the time of writing these instructions is 3.3.1).

## Install RStudio

Having RStudio is not absolutely necessary, but our course material
will follow a syntax that is close to RStudio's [R markdown](http://rmarkdown.rstudio.com/)
notation, so having RStudio will make our life easier. RStudio is also available for different operating systems. Pick the open source desktop edition from [here](http://www.rstudio.com/products/rstudio/download/) (the latest RStudio Desktop version at the time of writing these instructions is 0.99.902).

## Install JAGS

We will use JAGS during the course because it is robust, easy to install, and cross-paltform available. Download the latest version suitable for your operating system from [here](http://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/) (the latest JAGS version at the time of writing these instructions is 3.4.2).

> **Note**: due to recent changes in R's Windows toolchain (which impacts Windows specific installation only), pay attention to matching versions:
>
> * if you are using R 3.3.0 or later then install `JAGS-4.2.0-Rtools33.exe`,
> * if you are using R 3.2.4 or earlier then install `JAGS-4.2.0.exe`.

## Install R packages

Once R/RStudio and JAGS is installed, run the following commands in R/RStudio to install the necessary R packages ([rjags](https://cran.r-project.org/package=rjags),
[dclone](https://cran.r-project.org/package=dclone),
[coda](https://cran.r-project.org/package=code),
[snow](https://cran.r-project.org/package=snow),
[rlecuyer](https://cran.r-project.org/package=rlecuyer)):

```r
install.packages(c("rjags","dclone","coda","snow","rlecuyer"))
```

## Check that everything works as expected

Because there are dependencies and version requirements, best to check
that everything works. Please run the following code and follow the prompts:

```r
check_if_ready_for_the_course <-
function()
{
    if (getRversion() < "2.15.1")
        stop("R >= 2.15.1 required")
    cat("--- R version is",
        as.character(getRversion()), "--- OK\n")

    if (!require(dclone))
        stop("dclone package not installed")
    if (packageVersion("dclone") < "2.1.1")
        stop("dclone >= 2.1.1 required")
    cat("--- dclone package version is",
        as.character(packageVersion("dclone")), "--- OK\n")

    if (!require(coda))
        stop("coda package not installed")
    if (packageVersion("coda") < "0.13")
        stop("coda >= 0.13 required")
    cat("--- coda package version is",
        as.character(packageVersion("coda")), "--- OK\n")

    if (!require(rjags))
        stop("rjags package not installed")
    if (packageVersion("rjags") < "4.4")
        stop("rjags >= 4.4 required")
    cat("--- rjags package version is",
        as.character(packageVersion("rjags")), "--- OK\n")

    if (!require(snow))
        stop("snow package not installed")
    cat("--- snow package version is",
        as.character(packageVersion("snow")), "--- OK\n")

    if (!require(rlecuyer))
        stop("rlecuyer package not installed")
    cat("--- rlecuyer version is",
        as.character(packageVersion("rlecuyer")), "--- OK\n")

    cat("\n--- YOU ARE READY TO GO!\n\n")
    invisible(NULL)
}
check_if_ready_for_the_course()
```
Congratulations! Now your computer is ready for the course.

Contact [Peter Solymos](http://peter.solymos.org#about) if you still have problems.