There are many others of course such as my mood, whether or not I have a clue what you are talking about and what software I have been playing around with recently but that pretty much covers it.\u00a0 One application that I have started to recommend to people recently is called Simfit<\/a>.<\/p>\n What is Simifit?<\/strong><\/p>\n Simifit is a free<\/strong> piece of software written by Bill Bardsley of the University of Manchester.\u00a0 According to the application’s website<\/a> “Simfit is a computer package for simulation, statistical analysis, curve fitting and graph plotting<\/em>.”\u00a0 It is written for Windows but can also be run under Linux via WINE<\/a> (instructions specific to OpenSuse and KDE are given at this website<\/a>.)<\/p>\n Simfit actually consists of a suite of over forty individual programs but all of these are held together by one central ‘program manager’.\u00a0 Essentially you spend your Simfit life in the program manager and it will run the sub-programs as and when they are needed.\u00a0 It’s all very straightforward although, in my opinion, the graphical user interface isn’t as intuitive as most applications I have used.\u00a0 I guess I should qualify this somewhat – by ‘not as intuitive’ I mean ‘doesn’t quite behave like all other Windows applications’ and after speaking to Bill it seems that the reason for this is that he wanted to avoid anything that would make Simfit less stable or more memory hungry. \u00a0 His interface works well and all of his users are happy with it so why change?\u00a0 Furthermore, it hardly uses any memory at all and so Simfit will quite happily accept massive data sets that can bring other packages to their knees.\u00a0 It may be quirky but once you get used to it you’ll be fine.<\/p>\n Academic versus Professional versions <\/strong><\/p>\n Simfit comes in two flavours and both of them are free in the sense that Bill will charge you nothing for them.\u00a0 However one of them (The professional version<\/em>) has the NAG library as a pre-requisite and NAG costs money.\u00a0 If you (or your institution) has a license for the NAG Library then you are good to go and can happily use the professional version of Simfit at no extra charge.\u00a0 If, however,\u00a0 you don’t have a license for the NAG Library then you need to use the Academic version<\/em> which is also free but has less functionality. Details of the differences in functionality between the two versions can be found on the Simfit website<\/a>.<\/p>\n When you download Simfit you get both versions at the same time and the package comes with an utility that allows you to easily swap between the Academic and NAG library editions.<\/p>\n At this point, it might be worth mentioning that if you desperately need some functionality that is only available in the professional version then you can obtain a trial version of the NAG library from NAG themselves.<\/p>\n Installation<\/strong><\/p>\n Simfit works perfectly on just about any version of Windows you care to mention – Windows 95, 98, XP and Vista to name a few.\u00a0 I haven’t had chance to try it out on the new Windows 7 beta yet but I know one thing for sure – if it doesn’t work initially then I’ll bet my last dollarpound that Bill will get it working very quickly.\u00a0 He has put a lot of effort into ensuring that Simfit is portable across Windows versions and it shows.<\/p>\n In order to use all of Simfit’s features you will need to install a few pre-requisites first but happily all of them are free and Bill has made most of them conveniently available from his website.\u00a0 I installed things in the following order.<\/p>\n For .eps file support you need the following<\/p>\n For pdf viewing support you need<\/p>\n If you want to use Simfit in full ‘professional’ mode then you will need to install the commercial NAG libraries.\u00a0 If you don’t have a license the NAG library then don’t worry about it – Simfit will still work but with a few less bells and whistles.<\/p>\n Finally, you install Simfit itself using simfit_setup.exe.\u00a0 The installer is so quick and easy that I won’t insult your intelligence by going through it blow by blow.\u00a0 If you forget to install any of the pre-requisites then don’t worry – you can still install Simfit and simply add the other packages if and when you need them.<\/p>\n Plotting Graphs in Simfit<\/strong><\/p>\n Let’s start out with one of the (mathematically) simplest things that Simfit can do – plotting.\u00a0 They say that a picture can speak a thousand words so here are four plots produced with Simfit (taken from the author’s website<\/a>)<\/p>\n Simfit’s graphical output is in the widely used EPS format (encapsulated postscript<\/a>) which is of extremely high quality and easily incorporated into Latex<\/a> documents.\u00a0 An extra bonus that you get with EPS files is that they are actually nothing more than text files (well the ones produced by Simfit are at least) – you can open them up in something like Notepad and edit them by hand (if you know what you are doing).\u00a0 If you are unfortunate enough to be unable to use EPS files then Simift can convert them to a wide range of graphics formats including bmp, jpg, pcx, tiff and Windows quality emf.\u00a0 There is also a built in Postscript editor to manipulate eps files and create collages, insets etc.<\/p>\n Simfit has the capability to generate many different plot types including (among others) standard x-y line plots, 2 and 3D histograms, pie charts, box and whisker plots, Scree diagrams, Dendrogams, Scatchard plots,\u00a0 3D surface plots and contour plots. Phew!\u00a0 I don’t even know what some of these are.\u00a0 There are many other graphical facilities available but I think I will simply direct you to the author’s webpage<\/a> rather than repeat the full list here.<\/p>\n Statistical analysis with Simfit<\/strong><\/p>\n In its early days, Simfit only handled simulation<\/a> and curve fitting<\/a> but Bill and his collaborators felt that it would be useful to add an additional suite of statistical tests to the package.\u00a0 But which tests should be given priority?\u00a0 Bill’s approach was to speak to one of his collaborators, Tom Sharpe, a member of the Manchester University’s School of Biological Sciences (as it was called at the time).\u00a0 Tom drew up a list of all the statistical tests that had been used by the department over the previous few years and Bill implemented the lot!\u00a0 This formed the foundation of Simfit’s statistical abilities and Bill has been adding more routines ever since.<\/p>\n The full list of statistical routines is available on the Simfit website but, to save you a bit of clicking, I’ll reproduce a small sample<\/strong> of them here (shamelessly copied and pasted from the larger list here<\/a>)<\/p>\n Documentation<\/strong><\/p>\n It doesn’t matter how good a piece of software is if you can’t figure out how to use it and so good documentation is essential – especially for programs that contain advanced mathematics.\u00a0 Fortunatley Simfit is well served in this area as it comes with a beautifully produced manual.\u00a0 The manual has been typeset using Latex<\/a> and is accessible from the Windows start menu in either pdf or ps format.\u00a0 Bill even makes the manual’s full Latex source code available from the Simfit website (in the downloads section<\/a>) so you can compile it from source if you wish. The pdf file is very easy to navigate since it comes with a full table of contents and is extensively hyper-linked.<\/p>\n Weighing in at 425 pages (at the time of writing) it is certainly comprehensive but it is also very clearly written – Bill’ls multi-decade experience of being a university lecturer clearly shining through.\u00a0 As far as I can tell, the manual contains a fully worked example for every single Simfit routine including a suitable dataset and the sample data sets are also built into Simfit itself as you might expect. \u00a0 In fact I think that this is more than just a software manual, it gives a nice introduction to some of the mathematics too.\u00a0 In all honesty I think that this is one of the best produced manuals for a free piece of software that I have ever seen and it gives commercial offerings a run for their money too.<\/p>\n Use of Simfit in the academic community<\/strong><\/p>\n If you do a quick google search for free software that can handle things such as curve fitting, statistical analysis and publication quality plots then you will quickly be overwhelmed with choices but which ones can you trust?\u00a0 If you are going to submit your results for publication in a peer-reviewed journal then you need to be really sure that the software you choose gives you the right answer.\u00a0 One way to measure confidence in a piece of software like this is to look in the scientific literature and see if other researchers are using and citing it (in a good way).<\/p>\n So,\u00a0 I did exactly that and discovered that Simfit has been used by hundreds of researchers for many years all over the world.\u00a0 Here is a completely random selection of scientific papers that have made use of Simfit calculations over the last few years.\u00a0 I have tried to work out exactly how they used the package and put this in bold at the end of each citation but bear in mind that my own knowledge of statistics is pitiful so I apologize if I have got anything wrong.<\/p>\n This is just a small sample of what I found but I think you get the idea.\u00a0 If you spend a bit of time searching on google scholar<\/a> then you will come up with many<\/strong> more.\u00a0 So, it seems that Simfit is definitely trusted and well used by many in the scientific community.<\/p>\n What if Simfit doesn’t have the routine you need?<\/strong><\/p>\n If you find yourself wanting to do some sort of analysis that isn’t in Simfit then simply email Bill and (politely) ask!\u00a0 If time permits then he may well help you out.<\/p>\n Spanish Version<\/strong><\/p>\n Simfit is used extensively in spain and a Spanish version of the program is maintained by a team in Salamanca.\u00a0 I don’t speak Spanish so can’t offer any comment on this except to say that it is fully endorsed by Bill (in fact he gives Simfit courses over in Salamanca) and that the url for the spanish version is http:\/\/simfit.usal.es\/<\/a><\/p>\n\n
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![\"Simfit](\"\/images\/stats\/simfit_plots.png\")
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