Practical statistics books for software engineers

Derek Jones from The Shape of Code

So you have read my (draft) book on evidence-based software engineering and want to learn more about the statistical techniques used, but are not interested lots of detailed mathematics. What books do I suggest?

All the following books are sitting on the shelf next to where I write (not that they get read that much these days).

Before I took the training wheels off my R usage, my general go to book was (I still look at it from time to time): “The R Book” by Crawley, second edition; “R in Action” by Kabacoff is a good general read.

In alphabetical subject order:

Categorical data: “Categorical Data Analysis” by Agresti, the third edition is a weighty tomb (in content and heaviness). Plenty of maths+example; more of a reference.

Compositional data: “Analyzing compositional data with R” by van den Boogaart and Tolosana-Delgado, is more or less the only book of its kind. Thankfully, it is quite good.

Count data: “Modeling count data” by Hilbe, may be more than you want to know about count data. Readable.

Circular data: “Circular statistics in R” by Pewsey, Neuhauser and Ruxton, is the only non-pure theory book available. The material seems to be there, but is brief.

Experiments: “Design and analysis of experiments” by Montgomery.

General: “Applied linear statistical models” by Kutner, Nachtsheim, Neter and Li, covers a wide range of topics (including experiments) using a basic level of mathematics.

Mixed-effects models: “Mixed-effects models in S and S-plus” by Pinheiro and Bates, is probably the book I prefer; “Mixed effects models and extensions in ecology with R” by Zuur, Ieno, Walker, Saveliev and Smith, is another view on an involved topic (plus lots of ecological examples).

Modeling: “Statistical rethinking” by McElreath, is full of interesting modeling ideas, using R and Stan. I wish I had some data to try out some of these ideas.

Regression analysis: “Applied Regression Analysis and Generalized Linear Models” by Fox, now in its third edition (I also have the second edition). I found this the most useful book, of those available, for a more detailed discussion of regression analysis. Some people like “Regression modeling strategies” by Harrell, but this does not appeal to me.

Survival analysis: “Introducing survival and event history analysis” by Mills, is a readable introduction covering everything; “Survival analysis” by Kleinbaum and Klein, is full of insights but more of a book to dip into.

Time series: The two ok books are: “Time series analysis and its application: with R examples” by Shumway and Stoffler, contains more theory, while “Time series analysis: with applications in R” by Cryer and Chan, contains more R code.

There are lots of other R/statistics books on my shelves (just found out I have 31 of Springer’s R books), some ok, some not so. I have a few ‘programming in R’ style books; if you are a software developer, R the language is trivial to learn (its library is another matter).

Suggestions for books covering topics I have missed welcome, or your own preferences (as a software developer).

Statistical techniques not needed to analyze software engineering data

Derek Jones from The Shape of Code

One of the methods I used to try to work out what statistical techniques were likely to be useful to software developers, was to try to apply techniques that were useful in other areas. Of course, applying techniques requires the appropriate data to apply them to.

Extreme value statistics are used to spot patterns in rare events, e.g., frequency of rivers over spilling their banks and causing extensive flooding. I have tried and failed to find any data where Extreme value theory might be applicable. There probably is some such data, somewhere.

The fact that I have spent a lot of time looking for data and failed to find particular kinds of data, suggests that occurrences are rare. If data needing a particular kind of analysis technique is rare, there is no point including a discussion of the technique in a book aimed at providing general coverage of material.

I have spent some time looking for data drawn from a zero-inflated Poisson distribution. Readers are unlikely to have ever heard of this and might well ask why I would be interested in such an obscure distribution. Well, zero-truncated Poisson distributions crop up regularly (the Poisson distribution applies to count data that starts at zero, when count data starts at one the zeroes are said to be truncated and the Poisson distribution has to be offset to adjust for this). There is a certain symmetry to zero-truncated/inflated (although the mathematics involved is completely different), plus there is probably a sunk cost effect (i.e., I have spent time learning about them, I am going to find the data).

I spotted a plot in a paper investigating record data structure usage in Racket, that looked like it might be well fitted by a zero-inflated Poisson distribution. Tobias Pape kindly sent me the data (number of record data structures having a given size), which I then failed miserably to fit to any kind of Poisson related distribution; see plot below; data points along red line through the plus symbols (code+data):

Number of Racket record data structures having a given size.

I can only imagine what the authors thought of my reason for wanting the data (I made data requests to a few other researchers for similar reasons; and again I failed to fit the desired distribution).

I had expected to make more use of time series analysis; but, it has just not been that applicable.

Machine learning is useful for publishing papers, but understanding what is going on is the subject of my book, not building black boxes to make predictions.

It is possible that researchers are not publishing work relating to data that requires statistical techniques I have not used, because they don’t know how to analyze the data or the data is too hard to collect. Inability to use the correct techniques to analyze data is rarely a reason for not publishing a paper. Data being too hard to collect is very believable, as-is the data rarely occurring in software engineering related work.

There are statistical tests I have intentionally ignored, the Mann–Whitney U test (aka, the Wilcoxon rank-sum test) and the t-test probably being the most well-known. These tests became obsolete once computers became generally available. If you are ever stuck on a desert island without a computer, these are the statistical tests you will have to use.

What statistical techniques are useful for software engineering data?

Derek Jones from The Shape of Code

What statistical techniques are of general usefulness for analyzing software engineering data?

The answer depends on the kinds of data likely to be encountered, in software engineering, and the questions likely to be asked.

When I started working on a book, aiming to cover all worthwhile publicly available software engineering data, I was hoping to refer readers to a book (or two) that they ought to read to learn the appropriate techniques. Kabacoff’s “R in Action” comes closest to the book I had in mind as a basic introduction, but there was nothing covering a wider range of topics; so I ended up writing something; I found Crawley’s “The R book”, to be the best book on the subject.

My answer to the kinds of data likely to be available was to work with all the software engineering data I could get obtain (around 600 data sets to date).

What questions should be asked about the data? My selection of questions was driven by whether the data was used in the software engineering half of the book, or the statistical analysis techniques half.

The software engineering material consists of the chapters: Introduction, Human cognitive characteristics, Cognitive capitalism, Ecosystems, Projects, Reliability and Source code. The data appeared in one of these chapters if it could be used to make (what I thought was) a practical point about the topic being discussed.

Data appeared in the statistical analysis techniques chapters, if it could be used to illustrate the technique under discussion.

What happened in practice was the software engineering material was worked on for a year or two, on realizing that bespoke statistical analysis material was needed the existing data was plundered to create the necessary chapters; after this was released, work switched back to the software engineering material (using unplundered and newly acquired data), and of course the earlier chapters plundered data from the yet to be worked on chapters.

This seems to have worked surprisingly well, at least from my perspective of keeping the production line going.

Now most if the data has been analyzed, it’s time to take a global overview and where necessary shuffle things around. I may find that everything is a complete mess; we shall see.

What techniques have I found to be useful?

The number 1, most useful data analysis technique is building a regression model. The one thing I have been consistently able to do, when analyzing other people’s data, is extract more information from it than they did (unless they also built a regression model); at times it has been embarrassing.

At number 2, is bootstrapping. Many widely used techniques only give accurate answers if the data has a normal/gaussian distribution and use of these techniques can involve a lot of arm waving involving claims about the data having a good-enough gaussian-like distribution. This arm waving was necessary before computers became available, because the practical manual techniques required a gaussian distribution. Now we have computers and techniques that don’t require any particular distribution can be used, and which in some cases are more powerful techniques than those designed for manual implementation.

Sitting here, I cannot think of a number 3; there might be one.

What techniques are not generally useful? The various tests containing some combination of the names Wilcoxon, Mann and Whitney are well past their sell-by date. Searching the source of the book I see these names still appear in one or two places; this is a hangover from the early versions from many years ago (when I was following the clueless herd) and will soon be gone.

I thought that extreme value theory might apply to some data, but have only found one data-set to which it might be applied (so not generally useful).

I spent a lot of time watching out for zero-inflated data (data containing more zero values than expected by the common probability distributions). I saw four/five papers containing plots of data that looked zero-inflated and emailed the authors asking for the data (who kindly sent it to me). None of the data turned out to be zero-inflated (I’m not sure what the authors thought about being asked for data that somebody thought was zero-inflated). This does not mean that software engineering data is not zero-inflated, only that it is not common.

My zero-inflated search was motivated by the occasional appearance of zero-truncated data (data with that does not contain zero values). Zero-truncated data occurs when counting starts at one, rather than zero (I have one data-set that is 0/1 truncated; the counting starts at 2).

I was surprised that time-series did not turn out to be widely useful.

Sometimes we are all clueless button pushers, so machine learning gets a few pages. Anybody who knows what they are doing builds regression models.

I will eventually get around to counting how many times each technique is used on the data I have (watch this blog, but don’t hold your breath).