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Tutorial Setup
Phillip Alday, Douglas Bates, Reinhold Kliegl
February 17-19, 2020

A tutorial on Mixed Models in the Julia Programming Language will be held February 17-19, 2020 at the Zentrum fur interdisziplinare Forschung (ZiF) at the University of Bielefeld. In preparation for this tutorial, please follow these instructions to install Julia on the computer you will be using.

We assume that those participating in the tutorial are somewhat familiar with R and the RStudio IDE (integrated development environment).

Installing Julia

The Julia download site provides binary downloads for most common operating systems. Ensure that the version you install is at least v1.3.1. Version 1.4.0-rc1 (release candidate 1) is also suitable if you want to be in the vanguard.

The Julia REPL

By itself the Julia binary provides a basic REPL (read-eval-print-loop), which is quite adequate for installing packages. (Installing and using IDE's for Julia is discussed below.) When you start Julia you are in julia mode, as indicated by the julia> prompt.

Typing certain characters as the first in an input line will change the mode of the REPL.

Character Prompt Context
? help?> Help mode - print help messages on functions, types, etc.
] (v1.3) pkg> Pkg mode - install, list, remove, etc. packages
; shell> Shell mode - execute a single shell command
$ R> R mode - requires RCall package installed and active
<backspace> julia> return to Julia mode

Julia packages

The Standard Library

A binary installation of Julia includes several packages in the standard library. They are listed and documented as part of the general documentation at https://docs.julialang.org. Most of the time a user does not need to be conscious of these packages but occasionally we will attach one explicitly.

For example

julia> using InteractiveUtils, Random, Statistics

julia> varinfo(Random)   # list exported functions and types
  name                   size summary                   
  ––––––––––––––– ––––––––––– ––––––––––––––––––––––––––
  AbstractRNG       176 bytes DataType                  
  MersenneTwister   232 bytes DataType                  
  Random          478.102 KiB Module                    
  RandomDevice      192 bytes DataType                  
  bitrand             0 bytes typeof(Random.bitrand)    
  rand!               0 bytes typeof(Random.rand!)      
  randcycle           0 bytes typeof(Random.randcycle)  
  randcycle!          0 bytes typeof(Random.randcycle!) 
  randexp             0 bytes typeof(Random.randexp)    
  randexp!            0 bytes typeof(Random.randexp!)   
  randn!              0 bytes typeof(Random.randn!)     
  randperm            0 bytes typeof(Random.randperm)   
  randperm!           0 bytes typeof(Random.randperm!)  
  randstring          0 bytes typeof(Random.randstring) 
  randsubseq          0 bytes typeof(Random.randsubseq) 
  randsubseq!         0 bytes typeof(Random.randsubseq!)
  shuffle             0 bytes typeof(Random.shuffle)    
  shuffle!            0 bytes typeof(Random.shuffle!)   

julia> varinfo(Statistics)
  name              size summary                     
  –––––––––– ––––––––––– ––––––––––––––––––––––––––––
  Statistics 209.972 KiB Module                      
  cor            0 bytes typeof(Statistics.cor)      
  cov            0 bytes typeof(Statistics.cov)      
  mean           0 bytes typeof(Statistics.mean)     
  mean!          0 bytes typeof(Statistics.mean!)    
  median         0 bytes typeof(Statistics.median)   
  median!        0 bytes typeof(Statistics.median!)  
  middle         0 bytes typeof(Statistics.middle)   
  quantile       0 bytes typeof(Statistics.quantile) 
  quantile!      0 bytes typeof(Statistics.quantile!)
  std            0 bytes typeof(Statistics.std)      
  stdm           0 bytes typeof(Statistics.stdm)     
  var            0 bytes typeof(Statistics.var)      
  varm           0 bytes typeof(Statistics.varm)

User-contributed Packages

A listing of registered Julia packages is available at https://pkg.julialang.org/. Note the panel on the left where you can search by name or filter by tags on the packages. Packages we will use include

Name Purpose
CSV read and write comma-separated-value files
CategoricalArrays factor-like objects
DataFrames data tables with properties and capabilities like R's data.frame
DataFramesMeta database-like operations on data tables
IJulia Run Julia in Jupyter notebooks
MixedModels fit and examine mixed-effects models
PooledArrays light-weight version of categorical arrays
RCall call R from Julia, including data transfers
RData read data tables stored in .rda or .rds format
Tables general data table structures - either row- or column-oriented
Weave similar to the knitr package for R

These packages must be added (similar to package.install in R) before they can be attached with using (similar to library or require in R). In the package REPL (accessed by typing ] as the first character of a line) just type add Tables, for example. Note that you must have R installed on your computer to be able to successfully install the RCall package in Julia.

This document was created from the file README.jmd in this repository using Weave as


using Weave
weave("README.jmd", doctype="pandoc")

Integrated Development Environments

Editing and running Julia code is supported in both VSCode and the Atom editor. They are IDEs similar to RStudio. The VSCode support is documented at https://www.julia-vscode.org. The Atom support is called Juno and is documented at https://junolab.github.io. At least on some systems VSCode recognizes default installations of Julia and automatically sets the necessary paths. We recommend to start with installations of Julia and VSCode.

Either of these environments is fine for this workshop.

Jupyter notebooks

Jupyter provides interactive notebooks in the browser. When the IJulia package is installed and built it installs a version of conda if it is not already available. The jupyter-notebook and jupyter-lab applications can be added through conda. If you haven't used Jupyter notebooks it is probably best to wait to install them at the workshop.