Statistical computing with Scala free on-line course

I’ve recently delivered a three-day intensive short-course on Scala for statistical computing and data science. The course seemed to go well, and the experience has convinced me that Scala should be used a lot more by statisticians and data scientists for a range of problems in statistical computing. In particular, the simplicity of writing fast efficient parallel algorithms is reason alone to take a careful look at Scala. With a view to helping more statisticians get to grips with Scala, I’ve decided to freely release all of the essential materials associated with the course: the course notes (as PDF), code fragments, complete examples, end-of-chapter exercises, etc. Although I developed the materials with the training course in mind, the course notes are reasonably self-contained, making the course quite suitable for self-study. At some point I will probably flesh out the notes into a proper book, but that will probably take me a little while.

I’ve written a brief self-study guide to point people in the right direction. For people studying the material in their spare time, the course is probably best done over nine weeks (one chapter per week), and this will then cover material at a similar rate to a typical MOOC.

The nine chapters are:

1. Introduction
2. Scala and FP Basics
3. Collections
4. Scala Breeze
5. Monte Carlo
6. Statistical modelling
7. Tools
8. Apache Spark
9. Advanced topics

For anyone frustrated by the limitations of dynamic languages such as R, Python or Octave, this course should provide a good pathway to an altogether more sophisticated, modern programming paradigm.

MCMC as a Stream


This weekend I’ve been preparing some material for my upcoming Scala for statistical computing short course. As part of the course, I thought it would be useful to walk through how to think about and structure MCMC codes, and in particular, how to think about MCMC algorithms as infinite streams of state. This material is reasonably stand-alone, so it seems suitable for a blog post. Complete runnable code for the examples in this post are available from my blog repo.

A simple MH sampler

For this post I will just consider a trivial toy Metropolis algorithm using a Uniform random walk proposal to target a standard normal distribution. I’ve considered this problem before on my blog, so if you aren’t very familiar with Metropolis-Hastings algorithms, you might want to quickly review my post on Metropolis-Hastings MCMC algorithms in R before continuing. At the end of that post, I gave the following R code for the Metropolis sampler:

        vec=vector("numeric", n)
        for (i in 2:n) {
                if (log(runif(1)) < loga) { 

I will begin this post with a fairly direct translation of this algorithm into Scala:

def metrop1(n: Int = 1000, eps: Double = 0.5): DenseVector[Double] = {
    val vec = DenseVector.fill(n)(0.0)
    var x = 0.0
    var oldll = Gaussian(0.0, 1.0).logPdf(x)
    vec(0) = x
    (1 until n).foreach { i =>
      val can = x + Uniform(-eps, eps).draw
      val loglik = Gaussian(0.0, 1.0).logPdf(can)
      val loga = loglik - oldll
      if (math.log(Uniform(0.0, 1.0).draw) < loga) {
        x = can
        oldll = loglik
      vec(i) = x

This code works, and is reasonably fast and efficient, but there are several issues with it from a functional programmers perspective. One issue is that we have committed to storing all MCMC output in RAM in a DenseVector. This probably isn’t an issue here, but for some big problems we might prefer to not store the full set of states, but to just print the states to (say) the console, for possible re-direction to a file. It is easy enough to modify the code to do this:

def metrop2(n: Int = 1000, eps: Double = 0.5): Unit = {
    var x = 0.0
    var oldll = Gaussian(0.0, 1.0).logPdf(x)
    (1 to n).foreach { i =>
      val can = x + Uniform(-eps, eps).draw
      val loglik = Gaussian(0.0, 1.0).logPdf(can)
      val loga = loglik - oldll
      if (math.log(Uniform(0.0, 1.0).draw) < loga) {
        x = can
        oldll = loglik

But now we have two version of the algorithm. One for storing results locally, and one for streaming results to the console. This is clearly unsatisfactory, but we shall return to this issue shortly. Another issue that will jump out at functional programmers is the reliance on mutable variables for storing the state and old likelihood. Let’s fix that now by re-writing the algorithm as a tail-recursion.

def metrop3(n: Int = 1000, eps: Double = 0.5, x: Double = 0.0, oldll: Double = Double.MinValue): Unit = {
    if (n > 0) {
      val can = x + Uniform(-eps, eps).draw
      val loglik = Gaussian(0.0, 1.0).logPdf(can)
      val loga = loglik - oldll
      if (math.log(Uniform(0.0, 1.0).draw) < loga)
        metrop3(n - 1, eps, can, loglik)
        metrop3(n - 1, eps, x, oldll)

This has eliminated the vars, and is just as fast and efficient as the previous version of the code. Note that the @tailrec annotation is optional – it just signals to the compiler that we want it to throw an error if for some reason it cannot eliminate the tail call. However, this is for the print-to-console version of the code. What if we actually want to keep the iterations in RAM for subsequent analysis? We can keep the values in an accumulator, as follows.

def metrop4(n: Int = 1000, eps: Double = 0.5, x: Double = 0.0, oldll: Double = Double.MinValue, acc: List[Double] = Nil): DenseVector[Double] = {
    if (n == 0)
    else {
      val can = x + Uniform(-eps, eps).draw
      val loglik = Gaussian(0.0, 1.0).logPdf(can)
      val loga = loglik - oldll
      if (math.log(Uniform(0.0, 1.0).draw) < loga)
        metrop4(n - 1, eps, can, loglik, can :: acc)
        metrop4(n - 1, eps, x, oldll, x :: acc)

Factoring out the updating logic

This is all fine, but we haven’t yet addressed the issue of having different versions of the code depending on what we want to do with the output. The problem is that we have tied up the logic of advancing the Markov chain with what to do with the output. What we need to do is separate out the code for advancing the state. We can do this by defining a new function.

def newState(x: Double, oldll: Double, eps: Double): (Double, Double) = {
    val can = x + Uniform(-eps, eps).draw
    val loglik = Gaussian(0.0, 1.0).logPdf(can)
    val loga = loglik - oldll
    if (math.log(Uniform(0.0, 1.0).draw) < loga) (can, loglik) else (x, oldll)

This function takes as input a current state and associated log likelihood and returns a new state and log likelihood following the execution of one step of a MH algorithm. This separates the concern of state updating from the rest of the code. So now if we want to write code that prints the state, we can write it as

  def metrop5(n: Int = 1000, eps: Double = 0.5, x: Double = 0.0, oldll: Double = Double.MinValue): Unit = {
    if (n > 0) {
      val ns = newState(x, oldll, eps)
      metrop5(n - 1, eps, ns._1, ns._2)

and if we want to accumulate the set of states visited, we can write that as

  def metrop6(n: Int = 1000, eps: Double = 0.5, x: Double = 0.0, oldll: Double = Double.MinValue, acc: List[Double] = Nil): DenseVector[Double] = {
    if (n == 0) DenseVector(acc.reverse.toArray) else {
      val ns = newState(x, oldll, eps)
      metrop6(n - 1, eps, ns._1, ns._2, ns._1 :: acc)

Both of these functions call newState to do the real work, and concentrate on what to do with the sequence of states. However, both of these functions repeat the logic of how to iterate over the sequence of states.

MCMC as a stream

Ideally we would like to abstract out the details of how to do state iteration from the code as well. Most functional languages have some concept of a Stream, which represents a (potentially infinite) sequence of states. The Stream can embody the logic of how to perform state iteration, allowing us to abstract that away from our code, as well.

To do this, we will restructure our code slightly so that it more clearly maps old state to new state.

def nextState(eps: Double)(state: (Double, Double)): (Double, Double) = {
    val x = state._1
    val oldll = state._2
    val can = x + Uniform(-eps, eps).draw
    val loglik = Gaussian(0.0, 1.0).logPdf(can)
    val loga = loglik - oldll
    if (math.log(Uniform(0.0, 1.0).draw) < loga) (can, loglik) else (x, oldll)

The "real" state of the chain is just x, but if we want to avoid recalculation of the old likelihood, then we need to make this part of the chain’s state. We can use this nextState function in order to construct a Stream.

  def metrop7(eps: Double = 0.5, x: Double = 0.0, oldll: Double = Double.MinValue): Stream[Double] =
    Stream.iterate((x, oldll))(nextState(eps)) map (_._1)

The result of calling this is an infinite stream of states. Obviously it isn’t computed – that would require infinite computation, but it captures the logic of iteration and computation in a Stream, that can be thought of as a lazy List. We can get values out by converting the Stream to a regular collection, being careful to truncate the Stream to one of finite length beforehand! eg. metrop7().drop(1000).take(10000).toArray will do a burn-in of 1,000 iterations followed by a main monitoring run of length 10,000, capturing the results in an Array. Note that metrop7().drop(1000).take(10000) is a Stream, and so nothing is actually computed until the toArray is encountered. Conversely, if printing to console is required, just replace the .toArray with .foreach(println).

The above stream-based approach to MCMC iteration is clean and elegant, and deals nicely with issues like burn-in and thinning (which can be handled similarly). This is how I typically write MCMC codes these days. However, functional programming purists would still have issues with this approach, as it isn’t quite pure functional. The problem is that the code isn’t pure – it has a side-effect, which is to mutate the state of the under-pinning pseudo-random number generator. If the code was pure, calling nextState with the same inputs would always give the same result. Clearly this isn’t the case here, as we have specifically designed the function to be stochastic, returning a randomly sampled value from the desired probability distribution. So nextState represents a function for randomly sampling from a conditional probability distribution.

A pure functional approach

Now, ultimately all code has side-effects, or there would be no point in running it! But in functional programming the desire is to make as much of the code as possible pure, and to push side-effects to the very edges of the code. So it’s fine to have side-effects in your main method, but not buried deep in your code. Here the side-effect is at the very heart of the code, which is why it is potentially an issue.

To keep things as simple as possible, at this point we will stop worrying about carrying forward the old likelihood, and hard-code a value of eps. Generalisation is straightforward. We can make our code pure by instead defining a function which represents the conditional probability distribution itself. For this we use a probability monad, which in Breeze is called Rand. We can couple together such functions using monadic binds (flatMap in Scala), expressed most neatly using for-comprehensions. So we can write our transition kernel as

def kernel(x: Double): Rand[Double] = for {
    innov <- Uniform(-0.5, 0.5)
    can = x + innov
    oldll = Gaussian(0.0, 1.0).logPdf(x)
    loglik = Gaussian(0.0, 1.0).logPdf(can)
    loga = loglik - oldll
    u <- Uniform(0.0, 1.0)
} yield if (math.log(u) < loga) can else x

This is now pure – the same input x will always return the same probability distribution – the conditional distribution of the next state given the current state. We can draw random samples from this distribution if we must, but it’s probably better to work as long as possible with pure functions. So next we need to encapsulate the iteration logic. Breeze has a MarkovChain object which can take kernels of this form and return a stochastic Process object representing the iteration logic, as follows.


The steps method contains the logic of how to advance the state of the chain. But again note that no computation actually takes place until the foreach method is encountered – this is when the sampling occurs and the side-effects happen.

Metropolis-Hastings is a common use-case for Markov chains, so Breeze actually has a helper method built-in that will construct a MH sampler directly from an initial state, a proposal kernel, and a (log) target.

  metropolisHastings(0.0, (x: Double) =>
  Uniform(x - 0.5, x + 0.5))(x =>
  Gaussian(0.0, 1.0).logPdf(x)).

Note that if you are using the MH functionality in Breeze, it is important to make sure that you are using version 0.13 (or later), as I fixed a few issues with the MH code shortly prior to the 0.13 release.


Viewing MCMC algorithms as infinite streams of state is useful for writing elegant, generic, flexible code. Streams occur everywhere in programming, and so there are lots of libraries for working with them. In this post I used the simple Stream from the Scala standard library, but there are much more powerful and flexible stream libraries for Scala, including fs2 and Akka-streams. But whatever libraries you are using, the fundamental concepts are the same. The most straightforward approach to implementation is to define impure stochastic streams to consume. However, a pure functional approach is also possible, and the Breeze library defines some useful functions to facilitate this approach. I’m still a little bit ambivalent about whether the pure approach is worth the additional cognitive overhead, but it’s certainly very interesting and worth playing with and thinking about the pros and cons.

Complete runnable code for the examples in this post are available from my blog repo.

Books on Scala for statistical computing and data science


People regularly ask me about books and other resources for getting started with Scala for statistical computing and data science. This post will focus on books, but it’s worth briefly noting that there are a number of other resources available, on-line and otherwise, that are also worth considering. I particularly like the Coursera course Functional Programming Principles in Scala – I still think this is probably the best way to get started with Scala and functional programming for most people. In fact, there is an entire Functional Programming in Scala Specialization that is worth considering – I’ll probably discuss that more in another post. I’ve got a draft page of Scala links which has a bias towards scientific and statistical computing, and I’m currently putting together a short course in that area, which I’ll also discuss further in future posts. But this post will concentrate on books.

Reading list

Getting started with Scala

Before one can dive into statistical computing and data science using Scala, it’s a good idea to understand a bit about the language and about functional programming. There are by now many books on Scala, and I haven’t carefully reviewed all of them, but I’ve looked at enough to have an idea about good ways of getting started.

  • Programming in Scala: Third edition, Odersky et al, Artima.
    • This is the Scala book, often referred to on-line as PinS. It is a weighty tome, and works through the Scala language in detail, starting from the basics. Every serious Scala programmer should own this book. However, it isn’t the easiest introduction to the language.
  • Scala for the Impatient, Horstmann, Addison-Wesley.
    • As the name suggests, this is a much quicker and easier introduction to Scala than PinS, but assumes reasonable familiarity with programming in general, and sort-of assumes that the reader has a basic knowledge of Java and the JVM ecosystem. That said, it does not assume that the reader is a Java expert. My feeling is that for someone who has a reasonable programming background and a passing familiarity with Java, then this book is probably the best introduction to the language. Note that there is a second edition in the works.
  • Functional Programming in Scala Chiusano and Bjarnason, Manning.
    • It is possible to write Scala code in the style of "Java-without-the-semi-colons", but really the whole point of Scala is to move beyond that kind of Object-Oriented programming style. How much you venture down the path towards pure Functional Programming is very much a matter of taste, but many of the best Scala programmers are pretty hard-core FP, and there’s probably a reason for that. But many people coming to Scala don’t have a strong FP background, and getting up to speed with strongly-typed FP isn’t easy for people who only know an imperative (Object-Oriented) style of programming. This is the book that will help you to make the jump to FP. Sometimes referred to online as FPiS, or more often even just as the red book, this is also a book that every serious Scala programmer should own (and read!). Note that is isn’t really a book about Scala – it is a book about strongly typed FP that just "happens" to use Scala for illustrating the ideas. Consequently, you will probably want to augment this book with a book that really is about Scala, such as one of the books above. Since this is the first book on the list published by Manning, I should also mention how much I like computing books from this publisher. They are typically well-produced, and their paper books (pBooks) come with complimentary access to well-produced DRM-free eBook versions, however you purchase them.
  • Functional and Reactive Domain Modeling, Ghosh, Manning.
    • This is another book that isn’t really about Scala, but about software engineering using a strongly typed FP language. But again, it uses Scala to illustrate the ideas, and is an excellent read. You can think of it as a more practical "hands-on" follow-up to the red book, which shows how the ideas from the red book translate into effective solutions to real-world problems.
  • Structure and Interpretation of Computer Programs, second edition Abelson et al, MIT Press.
    • This is not a Scala book! This is the only book in this list which doesn’t use Scala at all. I’ve included it on the list because it is one of the best books on programming that I’ve read, and is the book that I wish someone had told me about 20 years ago! In fact the book uses Scheme (a Lisp derivative) as the language to illustrate the ideas. There are obviously important differences between Scala and Scheme – eg. Scala is strongly statically typed and compiled, whereas Scheme is dynamically typed and interpreted. However, there are also similarities – eg. both languages support and encourage a functional style of programming but are not pure FP languages. Referred to on-line as SICP this book is a classic. Note that there is no need to buy a paper copy if you like eBooks, since electronic versions are available free on-line.

Scala for statistical computing and data science

  • Scala for Data Science, Bugnion, Packt.
    • Not to be confused with the (terrible) book, Scala for machine learning by the same publisher. Scala for Data Science is my top recommendation for getting started with statistical computing and data science applications using Scala. I have reviewed this book in another post, so I won’t say more about it here (but I like it).
  • Scala Data Analysis Cookbook, Manivannan, Packt.
    • I’m not a huge fan of the cookbook format, but this book is really mis-named, as it isn’t really a cookbook and isn’t really about data analysis in Scala! It is really a book about Apache Spark, and proceeds fairly sequentially in the form of a tutorial introduction to Spark. Spark is an impressive piece of technology, and it is obviously one of the factors driving interest in Scala, but it’s important to understand that Spark isn’t Scala, and that many typical data science applications will be better tackled using Scala without Spark. I’ve not read this book cover-to-cover as it offers little over Scala for Data Science, but its coverage of Spark is a bit more up-to-date than the Spark books I mention below, so it could be of interest to those who are mainly interested in Scala for Spark.
  • Scala High Performance Programming, Theron and Diamant, Packt.
    • This is an interesting book, fundamentally about developing high performance streaming data processing algorithm pipelines in Scala. It makes no reference to Spark. The running application is an on-line financial trading system. It takes a deep dive into understanding performance in Scala and on the JVM, and looks at how to benchmark and profile performance, diagnose bottlenecks and optimise code. This is likely to be of more interest to those interested in developing efficient algorithms for scientific and statistical computing rather than applied data scientists, but it covers some interesting material not covered by any of the other books in this list.
  • Learning Spark, Karau et al, O’Reilly.
    • This book provides an introduction to Apache Spark, written by some of the people who developed it. Spark is a big data analytics framework built on top of Scala. It is arguably the best available framework for big data analytics on computing clusters in the cloud, and hence there is a lot of interest in it. The book is a perfectly good introduction to Spark, and shows most examples implemented using the Java and Python APIs in addition to the canonical Scala (Spark Shell) implementation. This is useful for people working with multiple languages, but can be mildly irritating to anyone who is only interested in Scala. However, the big problem with this (and every other) book on Spark is that Spark is evolving very quickly, and so by the time any book on Spark is written and published it is inevitably very out of date. It’s not clear that it is worth buying a book specifically about Spark at this stage, or whether it would be better to go for a book like Scala for Data Science, which has a couple of chapters of introduction to Spark, which can then provide a starting point for engaging with Spark’s on-line documentation (which is reasonably good).
  • Advanced Analytics with Spark, Ryza et al, O’Reilly.
    • This book has a bit of a "cookbook" feel to it, which some people like and some don’t. It’s really more like an "edited volume" with different chapters authored by different people. Unlike Learning Spark it focuses exclusively on the Scala API. The book basically covers the development of a bunch of different machine learning pipelines for a variety of applications. My main problem with this book is that it has aged particularly badly, as all of the pipelines are developed with raw RDDs, which isn’t how ML pipelines in Spark are constructed any more. So again, it’s difficult for me to recommend. The message here is that if you are thinking of buying a book about Spark, check very carefully when it was published and what version of Spark it covers and whether that is sufficiently recent to be of relevance to you.


There are lots of books to get started with Scala for statistical computing and data science applications. My "bare minimum" recommendation would be some generic Scala book (doesn’t really matter which one), the red book, and Scala for data science. After reading those, you will be very well placed to top-up your knowledge as required with on-line resources.

Scala for Data Science [book review]

This post will review the book:

Disclaimer: This book review has not been solicited by the publisher (or anyone else) in any way. I purchased the review copy of this book myself. I have not received any benefit from the writing of this review.


On this blog I previously reviewed the (terrible) book, Scala for machine learning by the same publisher. I was therefore rather wary of buying this book. But the topic coverage looked good, so I decided to buy it, and wasn’t disappointed. Scala for Data Science is my top recommendation for getting started with statistical computing and data science applications using Scala.


The book assumes a basic familiarity with programming in Scala, at around the level of someone who has completed the Functional Programming Principles in Scala Coursera course. That is, it (quite sensibly) doesn’t attempt to teach the reader how to program in Scala, but rather how to approach the development of data science applications using Scala. It introduces more advanced Scala idioms gradually (eg. typeclasses don’t appear until Chapter 5), so it is relatively approachable for those who aren’t yet Scala experts. The book does cover Apache Spark, but Spark isn’t introduced until Chapter 10, so it isn’t “just another Spark book”. Most of the book is about developing data science applications in Scala, completely independently of Spark. That said, it also provides one of the better introductions to Spark, so doubles up as a pretty good introductory Spark book, in addition to being a good introduction to the development of data science applications with Scala. It should probably be emphasised that the book is very much focused on data science, rather than statistical computing, but there is plenty of material of relevance to those who are more interested in statistical computing than applied data science.

Chapter by chapter

  1. Scala and Data Science – motivation for using Scala in preference to certain other languages I could mention…
  2. Manipulating data with BreezeBreeze is the standard Scala library for scientific and statistical computing. It’s pretty good, but documentation is rather lacking. This Chapter provides a good tutorial introduction to Breeze, which should be enough to get people going sufficiently to be able to make some sense of the available on-line documentation.
  3. Plotting with breeze-viz – Breeze has some support for plotting and visualisation of data. It’s somewhat limited when compared to what is available in R, but is fine for interactive exploratory analysis. However, the available on-line documentation for breeze-viz is almost non-existent. This Chapter is the best introduction to breeze-viz that I have seen.
  4. Parallel collections and futures – the Scala standard library has built-in support for parallel and concurrent programming based on functional programming concepts such as parallel (monadic) collections and Futures. Again, this Chapter provides an excellent introduction to these powerful concepts, allowing the reader to start developing parallel algorithms for multi-core hardware with minimal fuss.
  5. Scala and SQL through JDBC – this Chapter looks at connecting to databases using standard JVM mechanisms such as JDBC. However, it gradually introduces more functional ways of interfacing with databases using typeclasses, motivating:
  6. Slick – a functional interface for SQL – an introduction to the Slick library for a more Scala-esque way of database interfacing.
  7. Web APIs – the practicalities of talking to web APIs. eg. authenticated HTTP requests and parsing of JSON responses.
  8. Scala and MongoDB – working with a NoSQL database from Scala
  9. Concurrency with Akka – Akka is the canonical implementation of the actor model in Scala, for building large concurrent applications. It is the foundation on which Spark is built.
  10. Distributed batch processing with Spark – a tutorial introduction to Apache Spark. Spark is a big data analytics framework built on top of Scala and Akka. It is arguably the best available framework for big data analytics on computing clusters in the cloud, and hence there is a lot of interest in it. Indeed, Spark is driving some of the interest in Scala.
  11. Spark SQL and DataFrames – interfacing with databases using Spark, and more importantly, an introduction to Spark’s DataFrame abstraction, which is now fundamental to developing machine learning pipelines in Spark.
  12. Distributed machine learning with MLLib – MLLib is the machine learning library for Spark. It is worth emphasising that unlike many early books on Spark, this chapter covers the newer DataFrame-based pipeline API, in addition to the original RDD-based API. Together, Chapters 10, 11 and 12 provide a pretty good tutorial introduction to Spark. After working through these, it should be easy to engage with the official on-line Spark documentation.
  13. Web APIs with Play – is concerned with developing a web API at the end of a data science pipeline.
  14. Visualisation with D3 and the Play framework – is concerned with integrating visualisation into a data science web application.


This book provides a good tutorial introduction to a large number of topics relevant to statisticians and data scientists interested in developing data science applications using Scala. After working through this book, readers should be well-placed to augment their knowledge with readily searchable on-line documentation.

In a follow-up post I will give a quick overview of some other books relevant to getting started with Scala for statistical computing and data science.

First steps with monads in Scala


In the previous post I gave a quick introduction to some important concepts in functional programming, such as HOFs, closures, currying and partial application, and hopefully gave some insight into why these concepts might be useful in the context of scientific computing. Another concept that is very important in modern functional programming is that of the monad. Monads are one of those concepts that turns out to be very simple and intuitive once you “get it”, but completely impenetrable until you do! Now, there zillions of monad tutorials out there, and I don’t think that I have anything particularly insightful to add to the discussion. That said, most of the tutorials focus on problems and examples that are some way removed from the interests of statisticians and scientific programmers. So in this post I want to try and give a very informal and intuitive introduction to the monad concept in a way that I hope will resonate with people from a more scientific computing background.

The term “monad” is borrowed from that of the corresponding concept in category theory. The connection between functional programming and category theory is strong and deep. I intend to expore this more in future posts, but for this post the connection is not important and no knowledge of category theory is assumed (or imparted!).

Functors and Monads

Maps and Functors

All of the code used in this post in contained in the first-monads directory of my blog repo. The best way to follow this post is to copy-and-paste commands one-at-a-time from this post to a Scala REPL or sbt console. Note that only the numerical linear algebra examples later in this post require any non-standard dependencies.

The map method is one of the first concepts one meets when beginning functional programming. It is a higher order method on many (immutable) collection and other container types. Let’s start by looking at how map operates on Lists.

val x = (0 to 4).toList
// x: List[Int] = List(0, 1, 2, 3, 4)
val x2 = x map { x => x * 3 }
// x2: List[Int] = List(0, 3, 6, 9, 12)
val x3 = x map { _ * 3 }
// x3: List[Int] = List(0, 3, 6, 9, 12)
val x4 = x map { _ * 0.1 }
// x4: List[Double] = List(0.0, 0.1, 0.2, 0.30000000000000004, 0.4)

The last example shows that a List[T] can be converted to a List[S] if map is passed a function of type T => S. Of course there’s nothing particularly special about List here. It works with other collection types in the same way, as the following example with (immutable) Vector illustrates:

val xv = x.toVector
// xv: Vector[Int] = Vector(0, 1, 2, 3, 4)
val xv2 = xv map { _ * 0.2 }
// xv2: scala.collection.immutable.Vector[Double] = Vector(0.0, 0.2, 0.4, 0.6000000000000001, 0.8)
val xv3 = for (xi <- xv) yield (xi * 0.2)
// xv3: scala.collection.immutable.Vector[Double] = Vector(0.0, 0.2, 0.4, 0.6000000000000001, 0.8)

Note here that the for comprehension generating xv3 is exactly equivalent to the map call generating xv2 – the for-comprehension is just syntactic sugar for the map call. The benefit of this syntax will become apparent in the more complex examples we consider later.

Many collection and other container types have a map method that behaves this way. Any parametrised type that does have a map method like this is known as a Functor. Again, the name is due to category theory, but that doesn’t matter for this post. From a Scala-programmer perspective, a functor can be thought of as a trait, in pseudo-code as

trait F[T] {
  def map(f: T => S): F[S]

with F representing the functor. In fact it turns out to be better to think of a functor as a type class, but that is yet another topic for a future post… Also note that to be a functor in the strict sense (from a category theory perspective), the map method must behave sensibly – that is, it must satisfy the functor laws. But again, I’m keeping things informal and intuitive for this post – there are plenty of other monad tutorials which emphasise the category theory connections.

FlatMap and Monads

Once we can map functions over elements of containers, we soon start mapping functions which themselves return values of the container type. eg. we can map a function returning a List over the elements of a List, as illustrated below.

val x5 = x map { x => List(x - 0.1, x + 0.1) }
// x5: List[List[Double]] = List(List(-0.1, 0.1), List(0.9, 1.1), List(1.9, 2.1), List(2.9, 3.1), List(3.9, 4.1))

Clearly this returns a list-of-lists. Sometimes this is what we want, but very often we actually want to flatten down to a single list so that, for example, we can subsequently map over all of the elements of the base type with a single map. We could take the list-of-lists and then flatten it, but this pattern is so common that the act of mapping and then flattening is often considered to be a basic operation, often known in Scala as flatMap. So for our toy example, we could carry out the flatMap as follows.

val x6 = x flatMap { x => List(x - 0.1, x + 0.1) }
// x6: List[Double] = List(-0.1, 0.1, 0.9, 1.1, 1.9, 2.1, 2.9, 3.1, 3.9, 4.1)

The ubiquity of this pattern becomes more apparent when we start thinking about iterating over multiple collections. For example, suppose now that we have two lists, x and y, and that we want to iterate over all pairs of elements consisting of one element from each list.

val y = (0 to 12 by 2).toList
// y: List[Int] = List(0, 2, 4, 6, 8, 10, 12)
val xy = x flatMap { xi => y map { yi => xi * yi } }
// xy: List[Int] = List(0, 0, 0, 0, 0, 0, 0, 0, 2, 4, 6, 8, 10, 12, 0, 4, 8, 12, 16, 20, 24, 0, 6, 12, 18, 24, 30, 36, 0, 8, 16, 24, 32, 40, 48)

This pattern of having one or more nested flatMaps followed by a final map in order to iterate over multiple collections is very common. It is exactly this pattern that the for-comprehension is syntactic sugar for. So we can re-write the above using a for-comprehension

val xy2 = for {
  xi <- x
  yi <- y
} yield (xi * yi)
// xy2: List[Int] = List(0, 0, 0, 0, 0, 0, 0, 0, 2, 4, 6, 8, 10, 12, 0, 4, 8, 12, 16, 20, 24, 0, 6, 12, 18, 24, 30, 36, 0, 8, 16, 24, 32, 40, 48)

This for-comprehension (usually called a for-expression in Scala) has an intuitive syntax reminiscent of the kind of thing one might write in an imperative language. But it is important to remember that <- is not actually an imperative assignment. The for-comprehension really does expand to the pure-functional nested flatMap and map call given above.

Recalling that a functor is a parameterised type with a map method, we can now say that a monad is just a functor which also has a flatMap method. We can write this in pseudo-code as

trait M[T] {
  def map(f: T => S): M[S]
  def flatMap(f: T => M[S]): M[S]

Not all functors can have a flattening operation, so not all functors are monads, but all monads are functors. Monads are therefore more powerful than functors. Of course, more power is not always good. The principle of least power is one of the main principles of functional programming, but monads are useful for sequencing dependent computations, as illustrated by for-comprehensions. In fact, since for-comprehensions de-sugar to calls to map and flatMap, monads are precisely what are required in order to be usable in for-comprehensions. Collections supporting map and flatMap are referred to as monadic. Most Scala collections are monadic, and operating on them using map and flatMap operations, or using for-comprehensions is referred to as monadic-style. People will often refer to the monadic nature of a collection (or other container) using the word monad, eg. the “List monad”.

So far the functors and monads we have been working with have been collections, but not all monads are collections, and in fact collections are in some ways atypical examples of monads. Many monads are containers or wrappers, so it will be useful to see examples of monads which are not collections.

Option monad

One of the first monads that many people encounter is the Option monad (referred to as the Maybe monad in Haskell, and Optional in Java 8). You can think of it as being a strange kind of “collection” that can contain at most one element. So it will either contain an element or it won’t, and so can be used to wrap the result of a computation which might fail. If the computation succeeds, the value computed can be wrapped in the Option (using the type Some), and if it fails, it will not contain a value of the required type, but simply be the value None. It provides a referentially transparent and type-safe alternative to raising exceptions or returning NULL references. We can transform Options using map.

val three = Option(3)
// three: Option[Int] = Some(3)
val twelve = three map (_ * 4)
// twelve: Option[Int] = Some(12)

But when we start combining the results of multiple computations that could fail, we run into exactly the same issues as before.

val four = Option(4)
// four: Option[Int] = Some(4)
val twelveB = three map (i => four map (i * _))
// twelveB: Option[Option[Int]] = Some(Some(12))

Here we have ended up with an Option wrapped in another Option, which is not what we want. But we now know the solution, which is to replace the first map with flatMap, or better still, use a for-comprehension.

val twelveC = three flatMap (i => four map (i * _))
// twelveC: Option[Int] = Some(12)
val twelveD = for {
  i <- three
  j <- four
} yield (i * j)
// twelveD: Option[Int] = Some(12)

Again, the for-comprehension is a little bit easier to understand than the chaining of calls to flatMap and map. Note that in the for-comprehension we don’t worry about whether or not the Options actually contain values – we just concentrate on the “happy path”, where they both do, safe in the knowledge that the Option monad will take care of the failure cases for us. Two of the possible failure cases are illustrated below.

val oops: Option[Int] = None
// oops: Option[Int] = None
val oopsB = for {
  i <- three
  j <- oops
} yield (i * j)
// oopsB: Option[Int] = None
val oopsC = for {
  i <- oops
  j <- four
} yield (i * j)
// oopsC: Option[Int] = None

This is a typical benefit of code written in a monadic style. We chain together multiple computations thinking only about the canonical case and trusting the monad to take care of any additional computational context for us.

IEEE floating point and NaN

Those with a background in scientific computing are probably already familiar with the NaN value in IEEE floating point. In many regards, this value and the rules around its behaviour mean that Float and Double types in IEEE compliant languages behave as an Option monad with NaN as the None value. This is simply illustrated below.

val nan = Double.NaN
3.0 * 4.0
// res0: Double = 12.0
3.0 * nan
// res1: Double = NaN
nan * 4.0
// res2: Double = NaN

The NaN value arises naturally when computations fail. eg.

val nanB = 0.0 / 0.0
// nanB: Double = NaN

This Option-like behaviour of Float and Double means that it is quite rare to see examples of Option[Float] or Option[Double] in Scala code. But there are some disadvantages of the IEEE approach, as discussed elsewhere. Also note that this only works for Floats and Doubles, and not for other types, including, say, Int.

val nanC=0/0
// This raises a runtime exception!

Option for matrix computations

Good practical examples of scientific computations which can fail crop up frequently in numerical linear algebra, so it’s useful to see how Option can simplify code in that context. Note that the code in this section requires the Breeze library, so should be run from an sbt console using the sbt build file associated with this post.

In statistical applications, one often needs to compute the Cholesky factorisation of a square symmetric matrix. This operation is built into Breeze as the function cholesky. However the factorisation will fail if the matrix provided is not positive semi-definite, and in this case the cholesky function will throw a runtime exception. We will use the built in cholesky function to create our own function, safeChol (using a monad called Try which is closely related to the Option monad) returning an Option of a matrix rather than a matrix. This function will not throw an exception, but instead return None in the case of failure, as illustrated below.

import breeze.linalg._
def safeChol(m: DenseMatrix[Double]): Option[DenseMatrix[Double]] = scala.util.Try(cholesky(m)).toOption
val m = DenseMatrix((2.0, 1.0), (1.0, 3.0))
val c = safeChol(m)
// c: Option[breeze.linalg.DenseMatrix[Double]] =
// Some(1.4142135623730951  0.0
// 0.7071067811865475  1.5811388300841898  )

val m2 = DenseMatrix((1.0, 2.0), (2.0, 3.0))
val c2 = safeChol(m2)
// c2: Option[breeze.linalg.DenseMatrix[Double]] = None

A Cholesky factorisation is often followed by a forward or backward solve. This operation may also fail, independently of whether the Cholesky factorisation fails. There doesn’t seem to be a forward solve function directly exposed in the Breeze API, but we can easily define one, which I call dangerousForwardSolve, as it will throw an exception if it fails, just like the cholesky function. But just as for the cholesky function, we can wrap up the dangerous function into a safe one that returns an Option.

import com.github.fommil.netlib.BLAS.{getInstance => blas}
def dangerousForwardSolve(A: DenseMatrix[Double], y: DenseVector[Double]): DenseVector[Double] = {
  val yc = y.copy
  blas.dtrsv("L", "N", "N", A.cols, A.toArray, A.rows,, 1)
def safeForwardSolve(A: DenseMatrix[Double], y: DenseVector[Double]): Option[DenseVector[Double]] = scala.util.Try(dangerousForwardSolve(A, y)).toOption

Now we can write a very simple function which chains these two operations together, as follows.

def safeStd(A: DenseMatrix[Double], y: DenseVector[Double]): Option[DenseVector[Double]] = for {
  L <- safeChol(A)
  z <- safeForwardSolve(L, y)
} yield z

// res15: Option[breeze.linalg.DenseVector[Double]] = Some(DenseVector(0.7071067811865475, 0.9486832980505138))

Note how clean and simple this function is, concentrating purely on the “happy path” where both operations succeed and letting the Option monad worry about the three different cases where at least one of the operations fails.

The Future monad

Let’s finish with a monad for parallel and asynchronous computation, the Future monad. The Future monad is used for wrapping up slow computations and dispatching them to another thread for completion. The call to Future returns immediately, allowing the calling thread to continue while the additional thread processes the slow work. So at that stage, the Future will not have completed, and will not contain a value, but at some (unpredictable) time in the future it (hopefully) will (hence the name). In the following code snippet I construct two Futures that will each take at least 10 seconds to complete. On the main thread I then use a for-comprehension to chain the two computations together. Again, this will return immediately returning another Future that at some point in the future will contain the result of the derived computation. Then, purely for illustration, I force the main thread to stop and wait for that third future (f3) to complete, printing the result to the console.

import scala.concurrent.duration._
import scala.concurrent.{Future,ExecutionContext,Await}
val f1=Future{
  1 }
val f2=Future{
  2 }
val f3=for {
  v1 <- f1
  v2 <- f2
  } yield (v1+v2)

When you paste this into your console you should observe that you get the result in 10 seconds, as f1 and f2 execute in parallel on separate threads. So the Future monad is one (of many) ways to get started with parallel and async programming in Scala.


In this post I’ve tried to give a quick informal introduction to the monad concept, and tried to use examples that will make sense to those interested in scientific and statistical computing. There’s loads more to say about monads, and there are many more commonly encountered useful monads that haven’t been covered in this post. I’ve skipped over lots of details, especially those relating to the formal definitions of functors and monads, including the laws that map and flatMap must satisfy and why. But those kinds of details can be easily picked up from other monad tutorials. Anyone interested in pursuing the formal connections may be interested in a page of links I’m collating on category theory for FP. In particular, I quite like the series of blog posts on category theory for programmers. As I’ve mentioned in previous posts, I also really like the book Functional Programming in Scala, which I strongly recommend to anyone who wants to improve their Scala code. In a subsequent post I’ll explain how monadic style is relevant to issues relating to the statistical analysis of big data, as exemplified in Apache Spark. It’s probably also worth mentioning that there is another kind of functor that turns out to be exceptionally useful in functional programming: the applicative functor. This is more powerful than a basic functor, but less powerful than a monad. It turns out to be useful for computations which need to be sequenced but are not sequentially dependent (context-free rather than context-sensitive), and is a little bit more general and flexible than a monad in cases where it is appropriate.

Data frames and tables in Scala


To statisticians and data scientists used to working in R, the concept of a data frame is one of the most natural and basic starting points for statistical computing and data analysis. It always surprises me that data frames aren’t a core concept in most programming languages’ standard libraries, since they are essentially a representation of a relational database table, and relational databases are pretty ubiquitous in data processing and related computing. For statistical modelling and data science, having functions designed for data frames is much more elegant than using functions designed to work directly on vectors and matrices, for example. Trivial things like being able to refer to columns by a readable name rather than a numeric index makes a huge difference, before we even get into issues like columns of heterogeneous types, coherent handling of missing data, etc. This is why modelling in R is typically nicer than in certain other languages I could mention, where libraries for scientific and numerical computing existed for a long time before libraries for data frames were added to the language ecosystem.

To build good libraries for statistical computing in Scala, it will be helpful to build those libraries using a good data frame implementation. With that in mind I’ve started to look for existing Scala data frame libraries and to compare them.

A simple data manipulation task

For this post I’m going to consider a very simple data manipulation task: first reading in a CSV file from disk into a data frame object, then filtering out some rows, then adding a derived column, then finally writing the data frame back to disk as a CSV file. We will start by looking at how this would be done in R. First we need an example CSV file. Since many R packages contain example datasets, we will use one of those. We will export Cars93 from the MASS package:


If MASS isn’t installed, it can be installed with a simple install.packages("MASS"). The above code snippet generates a CSV file to be used for the example. Typing ?Cars93 will give some information about the dataset, including the original source.

Our analysis task is going to be to load the file from disk, filter out cars with EngineSize larger than 4 (litres), add a new column to the data frame, WeightKG, containing the weight of the car in KG, derived from the column Weight (in pounds), and then write back to disk in CSV format. This is the kind of thing that R excels at (pun intended):

df = df[df$EngineSize<=4.0,]
df$WeightKG = df$Weight*0.453592

Now let’s see how a similar task could be accomplished using Scala data frames.

Data frames and tables in Scala


Saddle is probably the best known data frame library for Scala. It is strongly influenced by the pandas library for Python. A simple Saddle session for accomplishing this task might proceed as follows:

val file = CsvFile("cars93.csv")
val df = CsvParser.parse(file).withColIndex(0)
val df2 = df.rfilter(_("EngineSize").
val wkg=df2.col("Weight").mapValues(CsvParser.parseDouble).
val df3=df2.joinPreserveColIx(wkg.mapValues(_.toString))

Although this looks OK, it’s not completely satisfactory, as the data frame is actually representing a matrix of Strings. Although you can have a data frame containing columns of any type, since Saddle data frames are backed by a matrix object (with type corresponding to the common super-type), the handling of columns of heterogeneous types always seems rather cumbersome. I suspect that it is this clumsy handling of heterogeneously typed columns that has motivated the development of alternative data frame libraries for Scala.


Scala-datatable is a lightweight minimal immutable data table for Scala, with good support for columns of differing types. However, it is currently really very minimal, and doesn’t have CSV import or export, for example. That said, there are several CSV libraries for Scala, so it’s quite easy to write functions to import from CSV into a datatable and write CSV back out from one. I’ve a couple of example functions, readCsv() and writeCsv() in the full code examples associated with this post. Now since datatable supports heterogeneous column types and I don’t want to write a type guesser, my readCsv() function expects information regarding the column types. This could be relaxed with a bit of effort. An example session follows:

    val colTypes=Map("DriveTrain" -> StringCol, 
                     "Min.Price" -> Double, 
                     "Cylinders" -> Int, 
                     "Horsepower" -> Int, 
                     "Length" -> Int, 
                     "Make" -> StringCol, 
                     "Passengers" -> Int, 
                     "Width" -> Int, 
                     "Fuel.tank.capacity" -> Double, 
                     "Origin" -> StringCol, 
                     "Wheelbase" -> Int, 
                     "Price" -> Double, 
                     "" -> Double, 
                     "Weight" -> Int, 
                     "Model" -> StringCol, 
                     "Max.Price" -> Double, 
                     "Manufacturer" -> StringCol, 
                     "EngineSize" -> Double, 
                     "AirBags" -> StringCol, 
                     "Man.trans.avail" -> StringCol, 
                     "" -> Double, 
                     "RPM" -> Int, 
                     "" -> Double, 
                     "MPG.highway" -> Int, 
                     "" -> Int, 
                     "Rev.per.mile" -> Int, 
                     "Type" -> StringCol)
    val df=readCsv("Cars93",new FileReader("cars93.csv"),colTypes)
    val df2=df.filter(row=>[Double]("EngineSize")<=4.0).toDataTable

    val oldCol=df2.columns("Weight").as[Int]
    val newCol=new DataColumn[Double]("WeightKG",{_.toDouble*0.453592})
    val df3=df2.columns.add(newCol).get

    writeCsv(df3,new File("out.csv"))

Apart from the declaration of column types, the code is actually a little bit cleaner than the corresponding Saddle code, and the column types are all properly preserved and appropriately handled. However, a significant limitation of this data frame is that it doesn’t seem to have special handling of missing values, requiring some kind of manually coded “special value” approach from users of this data frame. This is likely to limit the appeal of this library for general statistical and data science applications.


Framian is a full-featured data frame library for Scala, open-sourced by Pellucid analytics. It is strongly influenced by R data frame libraries, and aims to provide most of the features that R users would expect. It has good support for clean handling of heterogeneously typed columns (using shapeless), handles missing data, and includes good CSV import:

val df=Csv.parseFile(new File("cars93.csv")).labeled.toFrame
println(""+df.rows+" "+df.cols)
val df2=df.filter(Cols("EngineSize").as[Double])( _ <= 4.0 )
println(""+df2.rows+" "+df2.cols)
println(""+df3.rows+" "+df3.cols)
val csv = Csv.fromFrame(new CsvFormat(",", header = true))(df3)
new PrintWriter("out.csv") { write(csv.toString); close }

This is arguably the cleanest solution so far. Unfortunately the output isn’t quite right(!), as there currently seems to be a bug in Csv.fromFrame which causes the ordering of columns to get out of sync with the ordering of the column headers. Presumably this bug will soon be fixed, and if not it is easy to write a CSV writer for these frames, as I did above for scala-datatable.

Spark DataFrames

The three data frames considered so far are all standard single-machine, non-distributed, in-memory objects. The Scala data frame implementation currently subject to the most social media buzz is a different beast entirely. A DataFrame object has recently been added to Apache Spark. I’ve already discussed the problems of first developing a data analysis library without data frames and then attempting to bolt a data frame object on top post-hoc. Spark has repeated this mistake, but it’s still much better to have a data frame in Spark than not. Spark is a Scala framework for the distributed processing and analysis of huge datasets on a cluster. I will discuss it further in future posts. If you have a legitimate need for this kind of set-up, then Spark is a pretty impressive piece of technology (though note that there are competitors, such as flink). However, for datasets that can be analysed on a single machine, then Spark seems like a rather slow and clunky sledgehammer to crack a nut. So, for datasets in the terabyte range and above, Spark DataFrames are great, but for datasets smaller than a few gigs, it’s probably not the best solution. With those caveats in mind, here’s how to solve our problem using Spark DataFrames (and the spark-csv library) in the Spark Shell:

val df ="com.databricks.spark.csv").
                         option("header", "true").
val df2=df.filter("EngineSize <= 4.0")
val col=df2.col("Weight")*0.453592
val df3=df2.withColumn("WeightKG",col)


If you really need a distributed data frame library, then you will probably want to use Spark. However, for the vast majority of statistical modelling and data science tasks, Spark is likely to be unnecessarily complex and heavyweight. The other three libraries considered all have pros and cons. They are all largely one-person hobby projects, quite immature, and not currently under very active development. Saddle is fine for when you just want to add column headings to a matrix. Scala-datatable is lightweight and immutable, if you don’t care about missing values. On balance, I think Framian is probably the most full-featured “batteries included” R-like data frame, and so is likely to be most attractive to statisticians and data scientists. However, it’s pretty immature, and the dependence on shapeless may be of concern to those who prefer libraries to be lean and devoid of sorcery!

I’d be really interested to know of other people’s experiences of these libraries, so please do comment if you have any views, and especially if you have opinions on the relative merits of the different libraries.

The full source code for all of these examples, including sbt build files, can be found in a new github repo I’ve created for the code examples associated with this blog.

Calling Scala code from R using rscala


In a previous post I looked at how to call Scala code from R using a CRAN package called jvmr. This package now seems to have been replaced by a new package called rscala. Like the old package, it requires a pre-existing Java installation. Unlike the old package, however, it no longer depends on rJava, which may simplify some installations. The rscala package is well documented, with a reference manual and a draft paper. In this post I will concentrate on the issue of calling sbt-based projects with dependencies on external libraries (such as breeze).

On a system with Java installed, it should be possible to install the rscala package with a simple


from the R command prompt. Calling


will check that it has worked. The package will do a sensible search for a Scala installation and use it if it can find one. If it can’t find one (or can only find an installation older than 2.10.x), it will fail. In this case you can download and install a Scala installation specifically for rscala using the command


This option is likely to be attractive to sbt (or IDE) users who don’t like to rely on a system-wide scala installation.

A Gibbs sampler in Scala using Breeze

For illustration I’m going to use a Scala implementation of a Gibbs sampler. The Scala code, gibbs.scala is given below:

package gibbs

object Gibbs {

    import scala.annotation.tailrec
    import scala.math.sqrt
    import breeze.stats.distributions.{Gamma,Gaussian}

    case class State(x: Double, y: Double) {
      override def toString: String = x.toString + " , " + y + "\n"

    def nextIter(s: State): State = {
      val newX = Gamma(3.0, 1.0/((s.y)*(s.y)+4.0)).draw
      State(newX, Gaussian(1.0/(newX+1), 1.0/sqrt(2*newX+2)).draw)

    @tailrec def nextThinnedIter(s: State,left: Int): State =
      if (left==0) s else nextThinnedIter(nextIter(s),left-1)

    def genIters(s: State, stop: Int, thin: Int): List[State] = {
      @tailrec def go(s: State, left: Int, acc: List[State]): List[State] =
        if (left>0)
          go(nextThinnedIter(s,thin), left-1, s::acc)
          else acc

    def main(args: Array[String]) = {
      if (args.length != 3) {
        println("Usage: sbt \"run <outFile> <iters> <thin>\"")
      } else {
        val outF=args(0)
        val iters=args(1).toInt
        val thin=args(2).toInt
        val out = genIters(State(0.0,0.0),iters,thin)
        val s = new
        s.write("x , y\n")
        out map { it => s.write(it.toString) }


This code requires Scala and the Breeze scientific library in order to build. We can specify this in a sbt build file, which should be called build.sbt and placed in the same directory as the Scala code.

name := "gibbs"

version := "0.1"

scalacOptions ++= Seq("-unchecked", "-deprecation", "-feature")

libraryDependencies  ++= Seq(
            "org.scalanlp" %% "breeze" % "0.10",
            "org.scalanlp" %% "breeze-natives" % "0.10"

resolvers ++= Seq(
            "Sonatype Snapshots" at "",
            "Sonatype Releases" at ""

scalaVersion := "2.11.6"

Now, from a system command prompt in the directory where the files are situated, it should be possible to download all dependencies and compile and run the code with a simple

sbt "run output.csv 50000 1000"

sbt magically manages all of the dependencies for us so that we don’t have to worry about them. However, for calling from R, it may be desirable to run the code without running sbt. There are several ways to achieve this, but the simplest is to build an “assembly jar” or “fat jar”, which is a Java byte-code file containing all code and libraries required in order to run the code on any system with a Java installation.

To build an assembly jar first create a subdirectory called project (the name matters), an in it place two files. The first should be called assembly.sbt, and should contain the line

addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.13.0")

Since the version of the assembly tool can depend on the version of sbt, it is also best to fix the version of sbt being used by creating another file in the project directory called, which should contain the line


Now return to the parent directory and run

sbt assembly

If this works, it should create a fat jar target/scala-2.11/gibbs-assembly-0.1.jar. You can check it works by running

java -jar target/scala-2.11/gibbs-assembly-0.1.jar output.csv 10000 10

Assuming that it does, you are now ready to try running the code from within R.

Calling via R system calls

Since this code takes a relatively long time to run, calling it from R via simple system calls isn’t a particularly terrible idea. For example, we can do this from the R command prompt with the following commands

system("java -jar target/scala-2.11/gibbs-assembly-0.1.jar output.csv 50000 1000")

This works fine, but is a bit clunky. Tighter integration between R and Scala would be useful, which is where rscala comes in.

Calling assembly Scala projects via rscala

rscala provides a very simple way to embed a Scala interpreter within an R session, to be able to execute Scala expressions from R and to have the results returned back to the R session for further processing. The main issue with using this in practice is managing dependencies on external libraries and setting the Scala classpath correctly. By using an assembly jar we can bypass most of these issues, and it becomes trivial to call our Scala code direct from the R interpreter, as the following code illustrates.

sc%~%'import gibbs.Gibbs._'

Here we call the getIters function directly, rather than via the main method. This function returns an immutable List of States. Since R doesn’t understand this, we map it to an Array of Arrays, which R then unpacks into an R matrix for us to store in the matrix out.


The CRAN package rscala makes it very easy to embed a Scala interpreter within an R session. However, for most non-trivial statistical computing problems, the Scala code will have dependence on external scientific libraries such as Breeze. The standard way to easily manage external dependencies in the Scala ecosystem is sbt. Given an sbt-based Scala project, it is easy to generate an assembly jar in order to initialise the rscala Scala interpreter with the classpath needed to call arbitrary Scala functions. This provides very convenient inter-operability between R and Scala for many statistical computing applications.