Polished statistical analysis chapters in evidence-based software engineering

Derek Jones from The Shape of Code

I have completed the polishing/correcting/fiddling of the eight statistical analysis related chapters of my evidence-based software engineering book, and an updated draft pdf is now available (download here).

The material was in much better shape than I recalled, after abandoning it to the world 2-years ago, to work on the software engineering chapters.

Changes include moving more figures into the margin (which is responsible for a lot of the reduction in page count), fixing grammatical typos, removing place-holders for statistical techniques that are unlikely to be of general interest to software engineers, and mostly minor shuffling around (the only big change was moving a lot of material from the Experiments chapter to the Statistics chapter).

There is still some work to be done, in places (most notably the section on surveys).

What next? My collection of data waiting to be analysed has been piling up, so I will spend the next month reducing the backlog.

The six chapters covering the major areas of software engineering need to be polished and fleshed out, from their current bare-bones state. All being well, this time next year a beta release will be ready.

While working on the statistical material, I have been making monthly updates to the pdf+data available. If it makes sense to do this for the rest of the material, then it will happen. I’m not going to write a blog post every month; perhaps a post after what look like important milestones.

As always, if you know of any interesting software engineering data, please tell me.

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).

StatsModels: the first nail in R’s coffin

Derek Jones from The Shape of Code

In 2012, when I decided to write a book on evidence-based software engineering, R was the obvious system to use for data analysis. At the time, lots of new books had “using R” or “with R” added at the end of their titles; I chose “using R”.

When developers tell me they need to do some statistical analysis, and ask whether they should use Python or R, I tell them to use Python if statistics is a small part of the program, otherwise use R.

If I started work on the book today, I would till choose R. If I were starting five-years from now, I could be choosing Python.

To understand why I think Python will eventually take over the niche currently occupied by R, we need to understand the unique selling points of both systems.

R’s strengths are that it supports a way of thinking that is a good fit for doing data analysis and has an extensive collection of packages that simplify the task of applying a wide variety of analysis techniques to data.

Python also has packages supporting the commonly used data analysis techniques. But nearly all the Python packages provide a developer-mentality interface (i.e., they provide an API like any other package), R provides data-analysis-mentality interfaces. R supports a way of thinking that data analysts can identify with.

Python’s strengths, over R, are a much larger base of developers and language support for writing large programs (R is really a scripting language). Yes, Python has a package ecosystem supporting the full spectrum of application domains, this is not relevant for analysing a successful invasion of R’s niche market (but it is relevant for enticing new developers who are still making up their mind).

StatsModels is a Python package based around R’s data-analysis-mentality interface. When I discovered this package a few months ago, I realised the first nail had been hammered into R’s coffin.

Yes, today R has nearly all the best statistical analysis packages and a large chunk of the leading edge stuff. But packages can be reimplemented (C code can be copy-pasted, the R code mapped to Python); there is no magic involved. Leading edge has a short shelf life, and what proves to be useful can be duplicated; the market for leading edge code in a mature market (e.g., data analysis) is tiny.

A bunch of bright young academics looking to make a name for themselves will see the major trees in the R forest have been felled. The trees in the Python data-analysis-mentality forest are still standing; all it takes is a few people wanting to be known as the person who implemented the Python package that everybody uses for XYZ analysis.

A collection of packages supporting the commonly (and eventually not so commonly) used data analysis techniques, with a data-analysis-mentality interface, removes a major selling point for using R. Python is a bigger developer market with support for many other application domains.

The flow of developers starting out with R will slow down, casual R users will have nothing to lose from switching when the right project comes along. There will be groups where everybody uses R and will continue to use R because that is what everybody else in the group uses. Ten-Twenty years from now R, developers could be working in a ghost town.

Source code chapter added to “Evidence-based software engineering using R”

Derek Jones from The Shape of Code

The Source Code chapter of my evidence-based software engineering book has been added to the draft pdf (download here).

This chapter has suffered from coming last and there is still lots of work to be done. Almost all the source code related data has been plundered to fill up earlier chapters. Some data did not make the cut-off for release of the draft; a global review will probably result in some data migrating back to this chapter.

When talking to developers about the book I am constantly being asked ‘what is empirical software engineering?’ My explanation uses the phrase ‘evidence-based’, which everybody seems to immediately understand. It is counterproductive having a title that has to be explained, so I have changed the title to “Evidence-based Software Engineering using R”.

What is the purpose of a chapter discussing source code in a book on evidence-based software engineering? Source code is obviously an essential component of the topics discussed in the other chapters, but what is so particular to source code that it could not be said elsewhere? Having spent most of my professional life studying source code, first as a compiler writer and then involved with static analysis, am I just being driven by an attachment to the subject?

My view of source code is very different from most other developers: when developers talk about code, they spend most of the time talking about how they do things, when I talk about code I spend most of the time talking about how other developers do things (I’m a mongrel writer of code). Developers’ blinkered view of code prevents them seeing bigger pictures. I take a Gricean view of code and refrain from using meaningless marketing terms such as maintainability, readability and testability.

I have lots of source code data of interest to compiler writers (who are not the target audience) and I have lots of data related to static analysis (tool developers are not the audience). The target audience is professional software developers and hopefully what has been written is of interest to that readership.

I have been promised all sorts of data. Hopefully some of it will arrive. If somebody tells you they promised to send me data, please encourage them to take some time to sort out the data and send it.

As always, if you know of any interesting software engineering data, please tell me.

Finalizing the statistical analysis material in the second half of the book (released almost two years ago) next.

Reliability chapter added to “Empirical software engineering using R”

Derek Jones from The Shape of Code

The Reliability chapter of my Empirical software engineering book has been added to the draft pdf (download here).

I have been working on this draft for four months and it still needs lots of work; time to move on and let it stew for a while. Part of the problem is lack of public data; cost and schedule overruns can be rather public (projects chapter), but reliability problems are easier to keep quiet.

Originally there was a chapter covering reliability and another one covering faults. As time passed, these merged into one. The material kept evaporating in front of my eyes (around a third of the initial draft, collected over the years, was deleted); I have already written about why most fault prediction research is a waste of time. If it had not been for Rome I would not have had much to write about.

Perhaps what will jump out at people most, is that I distinguish between mistakes in code and what I call a fault experience. A fault_experience=mistake_in_code + particular_input. Most fault researchers have been completely ignoring half of what goes into every fault experience, the input profile (if the user does not notice a fault, I do not consider it experienced) . It’s incredibly difficult to figure out anything about the input profile, so it has been quietly ignored (one of the reasons why research papers on reported faults are such a waste of time).

I’m also missing an ‘interesting’ figure on the opening page of the chapter. Suggestions welcome.

I have not said much about source code characteristics. There is a chapter covering source code, perhaps some of this material will migrate to reliability.

All sorts of interesting bits and pieces have been added to earlier chapters. Ecosystems keeps growing and in years to come somebody will write a multi-volume tomb on software ecosystems.

I have been promised all sorts of data. Hopefully some of it will arrive.

As always, if you know of any interesting software engineering data, please tell me.

Source code chapter next.