Articles by nsaunders

Mapping data using R and leaflet

November 14, 2017 | 0 Comments

The R language provides many different tools for creating maps and adding data to them. I’ve been using the leaflet package at work recently, so I thought I’d provide a short example here. Whilst searching for some data that might make a nice map, I came across this ...
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XML parsing made easy: is that podcast getting longer?

October 12, 2017 | 0 Comments

Sometime in 2009, I began listening to a science podcast titled This Week in Virology, or TWiV for short. I thought it was pretty good and listened regularly up until sometime in 2016, when it seemed that most episodes were approaching two hours in duration. I listen to several podcasts when commuting ...
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Feels like a dry winter – but what does the data say?

October 11, 2017 | 0 Comments

A reminder that when idle queries pop into your head, the answer can often be found using R + online data. And a brief excursion into accessing the Weather Underground. One interesting aspect of Australian life, even in coastal urban areas like Sydney, is that sometimes it just stops raining. For ...
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Infographic-style charts using the R waffle package

September 7, 2017 | 0 Comments

Infographics. I’ve seen good examples. I’ve seen more bad examples. In general, I prefer a good chart to an infographic. That said, there’s a “genre” of infographic that I do think is useful, which I’ll call “if X were 100 Y”. A good example: if the world ...
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Years as coloured bars

August 5, 2017 | 0 Comments

I keep seeing years represented by coloured bars. First it was that demographic tsunami chart. Then there are examples like the one on the right, which came up in a web search today. I even saw one (whispers) at work today. I get what they are trying to do – illustrate ...
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Twitter Coverage of the ISMB/ECCB Conference 2017

August 2, 2017 | 0 Comments

ISMB (Intelligent Systems for Molecular Biology – which sounds rather old-fashioned now, doesn’t it?) is the largest conference for bioinformatics and computational biology. It is held annually and, when in Europe, jointly with the European Conference on Computational Biology (ECCB). I’ve had the good fortune to attend twice: in ...
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Twitter Coverage of the Bioinformatics Open Source Conference 2017

July 25, 2017 | 0 Comments

July 21-22 saw the 18th incarnation of the Bioinformatics Open Source Conference, which generally precedes the ISMB meeting. I had the great pleasure of attending BOSC way back in 2003 and delivering a short presentation on Bioperl. I knew almost nothing in those days, but everyone was very kind and appreciative. ...
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Hacking Highcharter: observations per group in boxplots

July 24, 2017 | 0 Comments

Highcharts has long been a favourite visualisation library of mine, and I’ve written before about Highcharter, my preferred way to use Highcharts in R. Highcharter has a nice simple function, hcboxplot(), to generate boxplots. I recently generated some for a project at work and was asked: can we see ...
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Chart golf: the “demographic tsunami”

July 20, 2017 | 0 Comments

“‘Demographic tsunami’ will keep Sydney, Melbourne property prices high” screams the headline. While the census showed Australia overall is aging, there’s been a noticeable lift in the number of people aged between 25 to 32. As the accompanying graph shows… Whoa, that is one ugly chart. First thought: let’s not ...
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Visualising Twitter coverage of recent bioinformatics conferences

June 20, 2017 | 0 Comments

Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the VIZBI 2017 meeting. So without further ado, here are the reports ...
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An update to the nhmrcData R package

March 15, 2017 | 0 Comments

Just pushed an updated version of my nhmrcData R package to Github. A quick summary of the changes: In response to feedback, added the packages required for vignette building as dependencies (Imports) – commit Added 8 new datasets with funding outcomes by gender for 2003 – 2013, created from a spreadsheet that I missed first … ...
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The nhmrcData package: NHMRC funding outcomes data made tidy

March 8, 2017 | 0 Comments

Do you like R? Information about Australian biomedical research funding outcomes? Tidy data? If the answers to those questions are “yes”, then you may also like nhmrcData, a collection of datasets derived from funding statistics provided by the Australian National Health & Medical Research Council. It’s also my first R ...
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HTML vignettes crashing your RStudio? This may be the reason

March 5, 2017 | 0 Comments

Short version: if RStudio on Windows 7 crashes when viewing vignettes in HTML format, it may be because those packages specify knitr::rmarkdown as the vignette engine, instead of knitr::knitr and you’re using rmarkdown v1. Longer version with details – read on. update: looks like this issue relates to the ...
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Twitter Coverage of the Lorne Genome Conference 2017

February 16, 2017 | 0 Comments

Things to know about Lorne in the state of Victoria, Australia. It’s situated on the Great Ocean Road, a major visitor attraction and a great way to see the scenic coastline of the region It’s home to a number of life science conferences including Lorne Genome 2017 This week’...
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Hyetographs, hydrographs and highcharter

February 6, 2017 | 0 Comments

Dual y-axes: yes or no? What about if one of them is also reversed, i.e. values increase from the top of the chart to the bottom? Judging by this StackOverflow question, hydrologists are fond of both of these things. It asks whether ggplot2 can be used to generate a “...
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Nice graphic? Are they taking the p…

February 4, 2017 | 0 Comments

Yes, it started with a tweet: Nice graphic on urine components via https://t.co/sfuXNB02sF pic.twitter.com/vhVLahQ8su — Metabolomics (@metabolomics) January 31, 2017 By what measure is this a “nice graphic”? First, the JPEG itself is low-quality. Second, it contains spelling and numerical errors (more on that later). ...
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The real meaning of spurious correlations

February 2, 2017 | 0 Comments

Like many data nerds, I’m a big fan of Tyler Vigen’s Spurious Correlations, a humourous illustration of the old adage “correlation does not equal causation”. Technically, I suppose it should be called “spurious interpretations” since the correlations themselves are quite real, but then good marketing is everything. There ...
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Taking steps (in XML)

February 1, 2017 | 0 Comments

So the votes are in: Your established blog is mostly about your work. Your work changes. Do you continue at the current blog or start a new one? — Neil Saunders (@neilfws) January 23, 2017 I thank you, kind readers. So here’s the plan: (1) keep blogging here as frequently as possible (perhaps ...
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Evidence for a limit to effective peer review

December 18, 2016 | 0 Comments

I missed it first time around but apparently, back in October, Nature published a somewhat-controversial article: Evidence for a limit to human lifespan. It came to my attention in a recent tweet: Just wow https://t.co/fupXIOAC43 pic.twitter.com/vsxT3VyTg6 — Nick Loman (@pathogenomenick) December 11, 2016 The source: a ...
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