books – ScraperWiki Extract tables from PDFs and scrape the web Tue, 09 Aug 2016 06:10:13 +0000 en-US hourly 1 58264007 Book review: The Tableau 8.0 Training Manual – From clutter to clarity by Larry Keller Tue, 27 Aug 2013 16:00:29 +0000 Tableau 8.0 Training Manual

My unstoppable reading continues, this time I’ve polished off The Tableau 8.0 Training Manual: From Clutter to Clarity by Larry Keller. This post is part review of the book, and part review of Tableau.

Tableau is a data visualisation application which grew out of academic research on visualising databases. I’ve used Tableau Public a little bit in the past. Tableau Public is a free version of Tableau which only supports public data i.e. great for playing around with but not so good for commercial work. Tableau is an important tool in the business intelligence area, useful for getting a quick view on data in databases and something our customers use, so we are interested in providing Tableau integration with the ScraperWiki platform.

The user interface for Tableau is moderately complex, hence my desire for a little directed learning. Tableau has a pretty good set of training videos and help pages online but this is no good to me since I do a lot of my reading on my commute where internet connectivity is poor.

Tableau is rather different to the plotting packages I’m used to using for data analysis. This comes back to the types of data I’m familiar with. As someone with a background in physical sciences I’m used to dealing with data which comprises a couple of vectors of continuous variables. So for example, if I’m doing spectroscopy then I’d expect to get a pair of vectors: the wavelength of light and the measured intensity of light at those wavelengths. Things do get more complicated than this, if I were doing a scattering experiment then I’d get an intensity and a direction (or possibly two directions). However, fundamentally the data is relatively straightforward.

Tableau is crafted to look at mixtures of continuous and categorical data, stored in a database table. Tableau comes with some sample datasets, one of which is sales data from superstores across the US which illustrates this well. This dataset has line entries of individual items sold with sale location data, product and customer (categorical) data alongside cost and profit (continuous) data. It is possible to plot continuous data but it isn’t Tableau’s forte.

Tableau expects data to be delivered in “clean” form, where “clean” means that spreadsheets and separated value files must be presented with a single header line with columns which contain data all of the same type. Tableau will also connect directly to a variety of databases. Tableau uses the Microsoft JET database engine to store it’s data, I know this because for some data unsightly wrangling is required to load data in the correct format. Once data is loaded Tableau’s performance is pretty good, I’ve been playing with the MOT data which is 50,000,000 or so lines, which for the range of operations I tried turned out to be fairly painless.

Turning to Larry Keller’s book, The Tableau 8.0 Training Manual: From Clutter to Clarity, this is one of few books currently available relating to the 8.0 release of Tableau. As described in the title it is a training manual, based on the courses that Larry delivers. The presentation is straightforward and unrelenting; during the course of the book you build 8 Tableau workbooks, in small, explicitly described steps. I worked through these in about 12 hours of screen time, and at the end of it I feel rather more comfortable using Tableau, if not expert. The coverage of Tableau’s functionality seems to be good, if not deep – that’s to say that as I look around the Tableau interface now I can at least say “I remember being here before”.

Some of the Tableau functionality I find a bit odd, for example I’m used to seeing box plots generated using R, or similar statistical package. From Clutter to Clarity shows how to make “box plots” but they look completely different. Similarly, I have a view as to what a heat map looks like and the Tableau implementation is not what I was expecting.

Personally I would have preferred a bit more explanation as to what I was doing. In common with Andy Kirk’s book on data visualisation I can see this book supplementing the presented course nicely, with the trainer providing some of the “why”. The book comes with some sample workbooks, available on request – apparently directly from the author whose email response time is uncannily quick.

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Book Review: Clean Code by Robert C. Martin Mon, 22 Jul 2013 16:31:20 +0000 Clean Code BookcoverFollowing my revelations regarding sharing code with other people I thought I’d read more about the craft of writing code in the form of Clean Code: A Handbook of Agile Software Craftmanship by Robert C. Martin.

Despite the appearance of the word Agile in the title this isn’t a book explicitly about a particular methodology or technology. It is about the craft of programming, perhaps encapsulated best by the aphorism that a scout always leaves a campsite tidier than he found it. A good programmer should leave any code they touch in a better state than they found it. Martin has firm ideas on what “better” means.

After a somewhat sergeant-majorly introduction in which Martin tells us how hard this is all going to be, he heads off into his theme.

Martin doesn’t like comments, he doesn’t like switch statements, he doesn’t like flag arguments, he doesn’t like multiple arguments to functions, he doesn’t like long functions, he doesn’t like long classes, he doesn’t like Hungarian* notation, he doesn’t like output arguments…

This list of dislikes generally isn’t unreasonable; for example comments in code are in some ways an anachronism from when we didn’t use source control and were perhaps limited in the length of our function names. The compiler doesn’t care about the comments and does nothing to police them so comments can be actively misleading (Guilty, m’lud). Martin prefers the use of descriptive function and variable names with a clear hierarchical structure to the use of comments.

The Agile origins of the book are seen with the strong emphasis on testing, and Test Driven Development. As a new convert to testing I learnt a couple of things here: clearly written tests being as important as clearly written code, the importance of test coverage (how much of you code is exercised by tests).

I liked the idea of structuring functions in a code file hierarchically and trying to ensure that each function operates at a single layer of abstraction, I’m fairly sold on the idea that a function should do one thing, and one thing only. Although to my mind the difficulty is in the definition of “thing”.

It seems odd to use Java as the central, indeed only, programming language in this book. I find it endlessly cluttered by keywords used in the specification of functions and variables, so that any clarity in the structure and naming that the programmer introduces is hidden in the fog. The book also goes into excruciating detail on specific aspects of Java in a couple of chapters. As a testament to the force of the PEP8 coding standard, used for Python, I now find Java’s prevailing use of CamelCase visually disturbing!

There are a number of lengthy examples in the book, demonstrating code before and after cleaning with a detailed description of the rationale for each small change. I must admit I felt a little sleight of hand was involved here, Martin takes chunks of what he considers messy code typically involving longish functions and breaks them down into smaller functions, we are then typically presented with the highest level function with its neat list of function calls. The tripling of the size of the code in function declaration boilerplate is then elided.

The book finishes with a chapter on “[Code] Smells and Heuristics” which summarises the various “code smells” (as introduced by Martin Fowler in his book Refactoring: Improving the Design of Existing Code) and other indicators that your code needs a cleaning. This is the handy quick reference to the lessons to be learned from the book. 

Despite some qualms about the style, and the fanaticism of it all I did find this an enjoyable read and felt I’d learnt something. Fundamentally I like the idea of craftsmanship in coding, and it fits with code sharing.

*Hungarian notation is the habit of appending letter or letters to variables to indicate their type.

Book review: Natural Language Processing with Python by Steven Bird, Ewan Klein & Edward Loper Tue, 25 Jun 2013 08:00:03 +0000 Natural-Language-Processing-with-PythonI bought Natural Language Processing in Python by Steven Bird, Ewan Klein & Edward Loper for a couple of reasons. Firstly, ScraperWiki are part of the EU Newsreader Project which seeks to make a “history recorder” using natural language processing to convert large streams of news articles into a more structured form. ScraperWiki’s role in this project is to scrape open sources of news related material, such as parliamentary records and to drive exploitation of the results of this work both commercially and through our contacts in the open source community. Although we’re not directly involved in the natural language processing work it seems useful to get a better understanding of the area.

Secondly, I’ve recently given a talk at Data Science London, and my original interpretation of the brief was that I should talk a bit about natural language processing. I know little of this subject so thought I should read up on it, as it turned out no natural language processing was required on my part.

This is the book of the Natural Language Toolkit Python library which contains a wide range of linguistic resources, methods for processing those resources, methods for accessing new resources and small applications to give a user-friendly interface for various features. In this context “resources” mean the full text of various books, corpora(large collections of text which have been marked up to varying degrees with grammatical and other data) and lexicons (dictionaries and the like).

Natural Language Processing is didactic, it is intended as a text for undergraduates with extensive exercises at the end of each chapter. As well as teaching the fundamentals of natural language processing it also seeks to teach readers Python. I found this second theme quite useful, I’ve been programming in Python for quite some time but my default style is FORTRANIC. The authors are a little scornful of this approach, they present some code I would have been entirely happy to write and describe it as little better than machine code! Their presentation of Python starts with list comprehensions which is unconventional, but goes on to cover the language more widely.

The natural language processing side of the book progresses from the smallest language structures (the structure of words), to part of speech labeling, phrases to sentences and ultimately deriving logical statements from natural language.

Perhaps surprisingly tokenization and segmentation, the process of dividing text into words and sentences respectively is not trivial. For example acronyms may contain full stops which are not sentence terminators. Less surprisingly part of speech (POS) tagging (i.e. as verb, noun, adjective etc) is more complex since words become different parts of speech in different contexts. Even experts sometimes struggle with parts of speech labeling. The process of chunking – identifying noun and verb phrases is of a similar character.

Both chunking and part of speech labeling are tasks which can be handled by machine learning. The zero order POS labeller assumes everything is a noun, the next simplest method is a simple majority voting one which takes the POS tag for previous word(s) and assumes the most frequent tag for the current word based on an already labelled body of text. Beyond this are the machine learning algorithms which take feature sets, including the tags of neighbouring words, to provide a best estimate of the tag for the word of interest. These algorithms include Bayesian classifiers, decision trees and the like, as discussed in Machine Learning in Action which I have previously reviewed. Natural Language Processing covers these topics fairly briefly but provides pointers to take things further, in particular highlighting that for performance reasons one may use external libraries from the Natural Language Toolkit library.

The final few chapters on context free grammars exceeded the limits of my understanding for casual reading, although the toy example of using grammars to translate natural language queries to SQL clarified the intention of these grammars for me. The book also provides pointers to additional material, and to where the limits of the field of natural language processing lie.

I enjoyed this book and recommend it, it’s well written with a style which is just the right level of formality. I read it on the train so didn’t try out as many of the code examples as I would have liked – more of this in future. You don’t have to buy this book, it is available online in its entirety but I think it is well worth the money.

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Book review: JavaScript: The Good Parts by Douglas Crockford Tue, 23 Apr 2013 08:47:06 +0000 JavaScript: The Good PartsThis week I’ve been programming in JavaScript, something of a novelty for me. Jealous of the Dear Leader’s automatically summarize tool I wanted to make something myself, hopefully a future post will describe my timeline visualising tool. Further motivations are that web scraping requires some knowledge of JavaScript since it is a key browser technology and, in its prototypical state, the ScraperWiki platform sometimes requires you to launch a console and type in JavaScript to do stuff.

I have two books on JavaScript, the one I review here is JavaScript: The Good Parts by Douglas Crockford – a slim volume which tersely describes what the author feels the best bits of JavaScript, incidently highlighting the bad bits. The second book is the JavaScript Bible by Danny Goodman, Michael Morrison, Paul Novitski, Tia Gustaff Rayl which I bought some time ago, impressed by its sheer bulk but which I am unlikely ever to read let alone review!

Learning new programming languages is easy in some senses: it’s generally straightforward to get something to happen simply because core syntax is common across many languages. The only seriously different language I’ve used is Haskell. The difficulty with programming languages is idiom, the parallel is with human languages: the barrier to making yourself understood in a language is low, but to speak fluently and elegantly needs a higher level of understanding which isn’t simply captured in grammar. Programming languages are by their nature flexible so it’s quite possible to write one in the style of another – whether you should do this is another question.

My first programming language was BASIC, I suspect I speak all other computer languages with a distinct BASIC accent. As an aside, Edsger Dijkstra has said:

[…] the teaching of BASIC should be rated as a criminal offence: it mutilates the mind beyond recovery.

  • so perhaps there is no hope for me.

JavaScript has always felt to me a toy language: it originates in a web browser and relies on HTML to import libraries but nowadays it is available on servers in the form of node.js, has a wide range of mature libraries and is very widely used. So perhaps my prejudices are wrong.

The central idea of JavaScript: The Good Parts is to present an ideal subset of the language, the Good Parts, and ignore the less good parts. The particular bad parts of which I was glad to be warned:

  • JavaScript arrays aren’t proper arrays with array-like performance, they are weird dictionaries;
  • variables have function not block scope;
  • unless declared inside a function variables have global scope;
  • there is a difference between the equality == and === (and similarly the inequality operators). The short one coerces and then compares, the longer one does not, and is thus preferred. 

I liked the railroad presentation of syntax and the section on regular expressions is good too.

Railroad syntax diagram - for statement

Elsewhere Crockford has spoken approvingly of CoffeeScript which compiles to JavaScript but is arguably syntactically nicer, it appears to hide some of the bad parts of JavaScript which Crockford identifies.

If you are new to JavaScript but not to programming then this is a good book which will give you a fine start and warn you of some pitfalls. You should be aware that you are reading about Crockford’s ideal not the code you will find in the wild.

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Book Review: Machine Learning in Action by Peter Harrington Wed, 17 Apr 2013 12:49:46 +0000 Machine Learning in ActionMachine learning is about prediction, and prediction is a valuable commodity. This sounds pretty cool and definitely the sort of thing a data scientist should be into, so I picked up Machine Learning in Action by Peter Harrington to get an overview of the area.

Amongst the examples covered in this book are:

  • Given that a customer bought these items, what other items are they likely to want?
  • Is my horse likely to die from colic given these symptoms?
  • Is this email spam?
  • Given that these representatives have voted this way in the past, how will they vote in future?

In order to make a prediction, machine learning algorithms take a set of features and a target for a training set of examples. Once the algorithm has been trained, it can take new feature sets and make predictions based on them. Let’s take a concrete example: if we were classifying birds, the birds’ features would include the weight, size, colour and so forth and the target would be the species. We would train the algorithm on an initial set of birds where we knew the species, then we would measure the features of unknown birds and submit these to the algorithm for classification.

In this case, because we know the target – a species of bird – the algorithms we use would be referred to as “supervised learning.” This contrasts “unsupervised learning,” where the target is unknown and the algorithm is seeking to make its own classification. This would be equivalent to the algorithm creating species of birds by clustering those with similar features. Classification is the prediction of categories (i.e. eye colour, like/dislike), alternatively regression is used to predict the value of continuous variables (i.e. height, weight).

Machine learning in Action is divided into four sections that cover key elements and “additional tools” which includes algorithms for dimension reduction and MapReduce – a framework for parallelisation. Dimension reduction is the process of identifying which features (or combination of features) are essential to a problem.

Each section includes Python code that implements the algorithms under discussion and these are applied to some toy problems. This gives the book the air of Numerical Recipes in FORTRAN, which is where I cut my teeth on numerical analysis. The mixture of code and prose is excellent for understanding exactly how an algorithm works, but its better to use a library implementation in real life.

The algorithms covered are:

  • Classification – k-Nearest Neighbours, decision trees, naive Bayes, logistic regression, support vector machines, and AdaBoost;
  • Regression – linear regression, locally weighted linear regression, ridge regression, tree-based regression;
  • Unsupervised learning – k-means clustering, apriori algorithm, FP-growth;
  • Additional tools – principle component analysis and singular value decomposition.

Prerequisites for this book are relatively high: it assumes fair Python knowledge, some calculus, probability theory and matrix algebra.

I’ve seen a lot of mention of MapReduce without being clear what it was. Now I am more clear: it is a simple framework for carrying out parallel computation. Parallel computing has been around quite some time, the problem has always been designing algorithms that accommodate parallelisation (i.e. allow problems to be broken up into pieces which can be solved separately and then recombined). MapReduce doesn’t solve this problem but gives a recipe for what is required to run on commodity compute cluster.

As Harrington says: do you need to run MapReduce on a cluster to solve your data problem? Unless you are an operation on the scale of Google or Facebook then probably not. Current, commodity desktop hardware is surprisingly powerful particularly when coupled with subtle algorithms.

This book works better as an eBook than paper partly because the paper version is black and white and some figures require colour but the programming listings are often images and so the text remains small.

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Book Review: Data Visualization: a successful design process by Andy Kirk Tue, 02 Apr 2013 10:43:01 +0000 Data Visualization CoverMy next review is of Andy Kirk’s book Data Visualization: a successful design process. Those of you on Twitter might know him as @visualisingdata, where you can follow his progress around the world as he delivers training. He also blogs at Visualising Data.

Previously in this area, I’ve read Tufte’s book The Visual Display of Quantitative Information and Nathan Yau’s Visualize ThisTufte’s book is based around a theory of effective visualisation whilst Visualize This is a more practical guide featuring detailed code examples. Kirk’s book fits between the two: it contains some material on the more theoretical aspects of effective visualisation as well as an annotated list of software tools; but the majority of the book covers the end-to-end design process.

Data Vizualisation introduced me to Anscombe’s Quartet. The Quartet is four small datasets, eleven (x,y) coordinate pairs in each. The Quartet is chosen so the common statistical properties (e.g. mean values of x and y, standard deviations for same, linear regression coefficients) for each set are identical, but when plotted they look very different. The numbers are shown in the table below.

Anscombe Quartet Data

Plotted they look like this:

Anscombe's QuartetAside from set 4, the numbers look unexceptional. However, the plots look strikingly different. We can easily classify their differences visually, despite the sets having the same gross statistical properties. This highlights the power of visualisation. As a scientist, I am constantly plotting the data I’m working on to see what is going on and as a sense check: eyeballing columns of numbers simply doesn’t work. Kirk notes that the design criteria for such exploratory visualisations are quite different from those highlighting particular aspects of a dataset, more abstract “data art” presentations, or a interactive visualisations prepared for others to use.

In contrast to the books by Tufte and Yau, this book is much more about how to do data visualisation as a job. It talks pragmatically about getting briefs from the client and their demands. I suspect much of this would apply to any design work.

I liked Kirk’s “Eight Hats of data visualisation design” metaphor; which name the skills a visualiser requires: Initiator, Data Scientist, Journalist, Computer Scientist, Designer, Cognitive Scientist, Communicator and Project Manager. In part, this covers what you will require to do data visualisation, but it also gives you an idea of whom you might turn to for help  –  someone with the right hat.

The book is scattered with examples of interesting visualisations, alongside a comprehensive taxonomy of chart types. Unsurprisingly, the chart types are classified in much the same way as statistical methods: in terms of the variable categories to be displayed (i.e. continuous, categorical and subdivisions thereof). There is a temptation here though: I now want to make a Sankey diagram… even if my data doesn’t require it!

In terms of visualisation creation tools, there are no real surprises. Kirk cites Excel first, but this is reasonable: it’s powerful, ubiquitous, easy to use and produces decent results as long as you don’t blindly accept defaults or get tempted into using 3D pie charts. He also mentions the use of Adobe Illustrator or Inkscape to tidy up charts generated in more analysis-oriented packages such as R. With a programming background, the temptation is to fix problems with layout and design programmatically which can be immensely difficult. Listed under programming environments is the D3 Javascript library, this is a system I’m interested in using  –  having had some fun with Protovis, a D3 predecessor.

Data Visualization works very well as an ebook. The figures are in colour (unlike the printed book) and references are hyperlinked from the text. It’s quite a slim volume which I suspect compliments Andy Kirk’s “in-person” courses well.

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Book Review: R in Action by Robert I. Kabacoff Wed, 27 Mar 2013 14:43:56 +0000 R in ActionThis is a review of Robert I. Kabacoff’s book R in Action which is a guided tour around the statistical computing package, R.

My reasons for reading this book were two-fold: firstly, I’m interested in using R for statistical analysis and visualisation. Previously I’ve used Matlab for this type of work, but R is growing in importance in the data science and statistics communities; and it is a better fit for the ScraperWiki platform. Secondly, I feel the need to learn more statistics. As a physicist my exposure to statistics is relatively slight  –  I’ve wondered why this is the case and I’m eager to learn more.

In both cases I see this book as an atlas for the area rather than an A-Z streetmap. I’m looking to find out what is possible and where to learn more rather than necessarily finding the detail in this book.

R in Action follows a logical sequence of steps for importing, managing, analysing, and visualising data for some example cases. It introduces the fundamental mindset of R, in terms of syntax and concepts. Central of these is the data frame  –  a concept carried over from other statistical analysis packages. A data frame is a collection of variables which may have different types (continuous, categorical, character). The variables form the columns in a structure which looks like a matrix  –  the rows are known as observations. A simple data frame would contain the height, weight, name and gender of a set of people. R has extensive facilities for manipulating and reorganising data frames (I particularly like the sound of melt in the reshape library).

R also has some syntactic quirks. For example, the dot (.) character, often used as a structure accessor in other languages, is just another character as far as R is concerned. The $ character fulfills a structure accessor-like role. Kabacoff sticks with the R user’s affection for using <- as the assignment operator instead of = which is what everyone else uses, and appears to work perfectly well in R.

R offers a huge range of plot types out-of-the-box, with many more a package-install away (and installing packages is a trivial affair). Plots in the base package are workman-like but not the most beautiful. I liked the kernel density plots which give smoothed approximations to histogram plots and the rug plots which put little ticks on the axes to show where the data in the body of that plot fall. These are all shown in the plot below, plotted from example data included in R.

Histogram, Rug and Density plot

The ggplot2 package provides rather more beautiful plots and seems to be the choice for more serious users of R.

The statistical parts of the book cover regression, power analysis, methods for handling missing data, group comparison methods (t-tests and ANOVA), and principle component and factor analysis, permutation and bootstrap methods. I found it a really useful survey  –  enough to get the gist and understand the principles with pointers to more in-depth information.

One theme running through the book, is that there are multiple ways of doing almost anything in R, as a result of its rich package ecosystem. This comes to something of a head with graphics in the final section: there are 4 different graphics systems with overlapping functionality but different syntax. This collides a little with the Matlab way of doing things where there is the one true path provided by Matlab alongside a fairly good, but less integrated, ecosystem of user-provided functionality.

R is really nice for this example-based approach because the base distribution includes many sample data sets with which to play. In addition, add-on packages often include sample data sets on which to experiment with the tools they provide. The code used in the book is all relatively short; the emphasis is on the data and analysis of the data rather than trying to build larger software objects. You can do an awful lot in a few lines of R.

As an answer to my statistical questions: it turns out that physics tends to focus on Gaussian-distributed, continuous variables, while statistics does not share this focus. Statistics is more generally interested in both categorical and continuous variables, and distributions cannot be assumed. For a physicist, experiments are designed where most variables are fixed, and the response of the system is measured as just one or two variables. Furthermore, there is typically a physical theory with which the data are fitted, rather than a need to derive an empirical model. These features mean that a physicist’s exposure to statistical methods is quite narrow.

Ultimately I don’t learn how to code by reading a book, I learn by solving a problem using the new tool  –  this is work in progress for me and R, so watch this space! As a taster, just half a dozen lines of code produced the appealing visualisation of twitter profiles shown below:



(Here’s the code:

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