Archive for April, 2010

SOFA Statistics and the “R is an Epic Fail” blog

Monday, April 26th, 2010

R is an open source programming language and software environment for statistics. And it is not just any old programming language – it is the dominant system for open source statistics. So was it fair to call R an “epic fail” as Dr. AnnMaria De Mars did in her notorious blog post The Next Big Thing?

Clearly R has been a massive success and it has a vibrant and lively community, many of whom were galvanised into making a response by the Epic Fail blog (see An article attacking R gets responses from the R blogosphere – some reflections on the phenomenon and R and the Next Big Thing as an example). So on what terms could it be considered a failure? For De Mars, successful software will be usable by the vast majority of people – not just programmers and others comfortable with command line interfaces.

… if you even LOOK at R code – bug-free or not, compilable or not – it should be evident that this is not how the average person uses a computer. If we are talking about something that is going to be used by a large number of people, R is not it (Comment by De Mars on her own blog post – The Next Big Thing).

… If your target market is “People who own cars that drive from point A to point B” that is much BIGGER than “people who work on engines”. If you are looking for a job making things or selling things or providing services, the former is more likely to pay off for you than the latter.
Telling people that if they can’t appreciate an internal combustion engine they are too stupid to own a car probably won’t help, either.” (The Next Big Thing).

And in these terms, De Mars has a point. For many users, R needs a GUI. I like this quote tweeted by ravkalia (a big fan of R BTW): “Overheard at a computing meeting: ‘R is not a programming language, it’s a statistics package with the GUI missing.’” Of course there are various projects to provide a GUI interface for R but it can be argued there are limits to how far that can go given the inherent flexibility of R as an environment. Yihui Xie recently commented – “I prefer the command-line due to its flexibility. GUI cannot hold infinite components (buttons, drop-lists, check-boxes, …), whereas there are almost infinite possibilities in commands.” (r-is-an-epic-fail).

On her other points regarding R and data visualisation, and analysis of enormous quantities of unstructured data, De Mars is on shakier ground, but the observations about the mainstream preference for looking and clicking are valid.

So how does this relate to SOFA Statistics? SOFA stands for Statistics Open For All, which gives a strong hint as to where SOFA is aiming in terms of user interfaces and target audience. In practice this means:

  1. A simple GUI. In practice, this means trying hard to leave the right things out rather than adding in every possible option. Sometimes less is more. Think about your TV remotes.
    Interface chaos

    Interface chaos

    Some commentators have implied that a GUI is not important because the sorts of people who do statistics will also be comfortable with basic programming. But this is not always true. And lots more people, by several orders of magnitude, need to run basic statistical analyses than just specialist statisticians. Karen Grace-Martin put it especially well in her response to the Epic Fail post:

    “I primarily help researchers, mainly in biology and social science, apply statistics to their research. They are not doing “business analytics,” do not have enormous databases, and really have no need to program anything beyond what SAS or SPSS syntax does. They are not programmers or statisticians, and they don’t have backgrounds in programming or math.

    I believe they are the kinds of users of statistics that you are referring to and I agree with you wholeheartedly that they are probably the majority of statistics users and they have no need for a programming language. They don’t want to nor need to program new statistical procedures.

    There are clearly people who do, but I agree they’re not the majority. At least not in the fields I work.” (The Next Big Thing).

    Even full-time specialist statisticians may find it easier to use a simple GUI for basic data exploration e.g. generating simple frequency tables and cross tabs. It has been suggested that people should expect to use more than one package (SPSS, SAS, R, Stata, JMP? Choosing a Statistical Software Package or Two) SOFA Statistics may be a useful complement to R for many users.

    And ease of use should not be premised on the assumption that people will be heavy users of the package – or of statistics in general, for that matter. The program needs to make it easy to become productive in a hurry.

  2. High priority on aesthetics. Output needs to look attractive; beautiful if possible.
    Lucid spirals demo

    Lucid spirals demo

    Even the program itself needs to look good:

    Form for selecting appropriate statistical test

    Form for selecting appropriate statistical test

  3. One True Way of Doing Things. It is not enough that there is a way of doing something – it can’t be buried somewhere obscure, and it has to clearly stand out as being correct and current (unlike some community technical advice).

    * In the Zen of Python (type import this into your Python interpreter) there is this gem: “There should be one– and preferably only one –obvious way to do it.”

  4. Helping the user when errors occur. Ideally, there would never be any errors but given there are it is important to make them as useful as possible. This is an ongoing project in SOFA Statistics which is being given a high priority. Error messages are an important part of the interface and one of the most important to get right. The better the error messages, the less support people need and the happier they are (under the circumstances). Jon Peck commented on an unhelpful error message he receives from R:

    Here is an error message that I get a lot from a popular R package.
    ‘Error in optim(0, f, control = control, hessian = TRUE, method = “BFGS”) :
    non-finite finite-difference value [1]‘
    I know what that means. Would an analyst?
    (Jon Peck – in response to The Next Big Thing)

  5. Not relying on users to stitch together everything they need. Ordinary users benefit if their application bundles together related output. This is a balancing act and one which we want to get right for the target user group for SOFA Statistics. The following quote captures the tradeoffs well:

    But one thing is clear to me: R aims at people who know what they are doing. Absolutely. You can see this with standard output in R which is very minimalistic. You must ASK R what you want from it. SAS and SPSS put everything out. And therefore you need to know how to program in R to use it, really. But if you do, you feel bound and limited with SAS or SPSS. (comment by mocianmomo in response to SAS v. R: Ease of learning).

  6. SOFA Statistics uses Python for Scripting. Python is a language consciously designed to be easy to learn. Many statisticians find it a pleasure to work with Python but the same is not always true of the syntax of many statistics packages, especially those with lots of historical cruft.
  7. Example SOFA script

    Example SOFA script in Python

0.9.9 attractive new output styles; easier to change styles; UI improvements

Saturday, April 24th, 2010

Although this latest release has many, many enhancements and fixes (full details below), the most pleasing change for most users will probably be the availability of some attractive new output styles. It is also easier to select and apply them.

The 3 new styles are:

  • Grey Spirals
    Grey spirals demo

    Grey spirals demo

  • Lucid Spirals
    Lucid spirals demo

    Lucid spirals demo

  • Pebbles
    Pebbles demo

    Pebbles demo

Output styles can be selected using a simple drop-down list.

Style selection

Style selection

The full list of new features is:

  • Added 3 attractive output styles – grey_spirals, lucid_spirals, and pebbles. These include background images.
  • Styles can be selected and changed much more easily.
  • Crosstabs with column totals and row percentages get a frequency in the total column even if frequency is not selected.
  • Customised waiting message when making report tables according to what is required e.g. “Add and configure column”.
  • Configuration settings (e.g. preferred output style) persist across all dialogs.
  • The last configured row summary measures are the default for any new variables added to the row summary report table.
  • The Expand button opens a much larger window to view content in.
  • Better display of html messages in report tables dialog.
  • Simplified standard names e.g. “SOFA_Default_db” became “sofa_db”.
  • Can resize some dialogs smaller than initial display size.
  • Application gives a useful error message, even if it fails very early.
  • Faster production of report tables by avoiding duplicate queries.
  • When adding row or col vars, can double click selections except for raw display tables or rows of row summary tables where still multichoice selections.
  • Removed windows manager close buttons from dialogs so program close buttons used instead.
  • Windows installer now installs Python 2.6.5 instead of 2.6.2.
  • Misc UI changes to make setting up MS connection details easier.

There have also been numerous bug fixes:

  • Debian package now uses desktop icon sofastats.desktop rather than sofa.desktop to prevent collision with sofa-apps.
  • Fixed bug when selecting default project to edit after having selected another. Would set proj dropdown to point to the first proj (more generally, the last one that was saved and was not read-only).
  • No longer possible to overwrite the default project with another of the same name.
  • In the report table dialog, the Add Under button for columns only shows when a column variable has already been selected.
  • Add Under button for rows disabled for Row Summaries.
  • Fixed bug where right clicking on a row or column variable in the report tables dialog tree didn’t shift selection to it.
  • Fixed bug where selection in report tables dialog row/column tree should shift to another item sibling but went nowhere.
  • Fixed bug if MS Access database selected multiple times. Needed to properly clear resources before getting them again.
  • Fixed bug running some statistical tests when variable includes % in name.
  • Fixed bug where unable to change cell values in strangely named tables e.g. ‘demo;’.
  • Fixed bug where some faulty values for DataDets would get through even if an error.
  • When faulty database selection made, e.g. MS SQL Server model, reverts to last selected database.

0.9.8 Viewing and organising output reports simplified

Friday, April 9th, 2010

The latest set of changes are the direct result of user input. A user emailed us to say he found working with the output reports a bit confusing and the end result was a better way of viewing and organising output reports.

So here’s how it works. If you start saving output, it goes into the default html report file. If you want it to go into an existing html file, you select that using Browse and it will be added there. And if you want to create a new output file, you can just browse to the correct folder and enter the file name. Pretty simple and flexible as well.

Make new output report

Make new output report

As for viewing output reports, it has always been possible to use your file manager to locate your output file and double click it (thus opening it as a tab in your default browser e.g. Firefox). Now it is much easier – just click on the new View button next to the report name and it will automatically open as a tab in your default browser.

New output view button

New output view button

Your output opened in your browser

Your output opened in your browser


Here is the list of main changes:

  • Can view output reports from SOFA Statistics using a View button. Clicking View opens the selected report as a fresh tab in the default web browser.
  • Can create new reports using the Browse button for reports by navigating to a folder and entering the name of the new report.
  • The four Browse buttons (e.g. for browsing reports) now have hover text help to explain what they are for.
  • Misc UI changes to make setting up MS connection details easier.

A few bugs were fixed as well and there was a major set of changes to prevent future bugs related to database connections:

  • Huge overhaul of approach to connecting to databases. Should be no detectable difference above the surface (apart from being slightly faster perhaps) but should prevent lots of bugs in the future.
  • Fixed bug where unable to change cell values in strangely named tables e.g. ‘demo;’
  • When faulty database selection made, e.g. MS SQL Server model, reverts to last selected database.