Blog Archives

How effective is my research programming workflow? The Philip Test – Part 1

March 10, 2014
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How effective is my research programming workflow? The Philip Test – Part 1

Philip Guo, who writes a wonderful blog on his views and experiences of academia – including a lot of interesting programming stuff – came up with a research programming version of The Joel Test last summer, and since then I’ve been thinking of writing a series commenting on how well I fulfil each of the items on

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Encouraging citation of software – introducing CITATION files

August 30, 2013
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Summary: Put a plaintext file named CITATION in the root directory of your code, and put information in it about how to cite your software. Go on, do it now – it’ll only take two minutes! Software is very important in science – but good software takes time and effort that could be used to do

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John Snow’s Cholera data in more formats

March 13, 2013
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John Snow’s Cholera data in more formats

In honour of the bicentenary of John Snow’s birth – and because I was asked to by someone via email – I have now released my digitisation of John Snow’s Cholera data in a few other formats: KML and as Google Fusion Tables. To save you reading my previous blog posts on the subject, I’ll

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In praise of ProjectTemplate for reproducible research

September 7, 2012
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In praise of ProjectTemplate for reproducible research

As you might know from some of my previous posts, I’m a big fan of making my scientific work reproducible. My main reasons for being so keen on this are: 1. Reproducibility is key to science – if it can’t be reproduced then it can not be verified (that is, the experiment can’t be tried again

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John Snow’s famous cholera analysis data in modern GIS formats

January 6, 2012
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John Snow’s famous cholera analysis data in modern GIS formats

In 1854 there was a massive cholera outbreak in Soho, London – in three days over 120 people died from the disease. Famously, John Snow plotted the locations of the deaths on a map and found they clustered around a pump in Broad Street – he suggested that the pump be taken out of service

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Please use sensible colours in your maps

November 2, 2011
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If you are creating maps then for goodness sake Use sensible colours!  I was helping some undergraduates with some work the other day, and they decided to use the following colour scheme for representing river depth: Deep water: Red Medium-depth water: Bright green Shallow water: Pink Why did they do this? Well, either they were

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My programming journey

May 20, 2011
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My programming journey

When clearing out some of my old programming books the other day I realised how far I’d come with programming over the years, and the number of different technologies that I have used over time. I thought I’d do a little summary post going from first programming experience to now – and it’s amazing what’s

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Review: R Graphs Cookbook by Hrishi Mittal

March 11, 2011
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Review: R Graphs Cookbook by Hrishi Mittal

Summary: Very useful for reference while producing graphs, and very comprehensive (including heat-maps, 3D graphs and maps). Reference: Mittal, H. V., 2011, R Graph Cookbook, Packt Publishing, Birmingham, UK, 272 pages,  Publisher’s Website As a scientist I often need to plot graphs of my data, so I am keen to learn more about how to

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Review: R in a Nutshell by Joseph Adler

January 17, 2011
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Review: R in a Nutshell by Joseph Adler

Summary: Very comprehensive and very useful, but not good for a beginner. Great book though – definitely has a place on my bookshelf. Reference: Adler, J., 2010, R in a Nutshell, O’Reilly, Sebastopol, CA, 611 pages  O’Reilly Link After reviewing a book about R designed for beginners (see my previous post) I thought I’d step

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Review: Statistical Analysis with R: Beginner’s Guide by John M. Quick

January 1, 2011
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Review: Statistical Analysis with R: Beginner’s Guide by John M. Quick

Summary: If you can get past the strange underlying story, then this gives a good introduction to R to someone with no programming experience. However, if you have any experience with other programming languages then another book is likely to be more suitable. Reference: Quick, J. M., Statistical Analysis in R: Beginners Guide, Packt Publishing,

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