Posted by nsaunders

Extracting data from news articles: Australian pollution by postcode

The recent ABC News article Australia’s pollution mapped by postcode reveals nation’s dirty truth is interesting. It contains a searchable table, which is useful if you want to look up your own suburb. However, I was left wanting more: specifically, the raw data and some nice maps. So … Continue reading →

Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.

You can file this one under “I may have the very specific solution if you’re having exactly the same problem.” So: if you’re running some R code and you see a warning like this: Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was … Continue reading →

Just use a scatterplot. Also, Sydney sprawls.

Dual-axes at tipping-pointSydney’s congestion at ‘tipping point’ blares the headline and to illustrate, an interactive chart with bars for city population densities, points for commute times and of course, dual-axes. Yuck. OK, I guess it does show that Sydney is one of three … Continue reading →

Using leaflet, just because

I love it when researchers take the time to share their knowledge of the computational tools that they use. So first, let me point you at Environmental Computing, a site run by environmental scientists at the University of New South Wales, which has a good selection of R programming tutorials. One … Continue reading →

Twitter coverage of the useR! 2018 conference

In summary: useR! the conference for users of R was held in Brisbane earlier this month it sounded like a lot of fun and here’s an analysis of tweets that used the #useR2018 hashtag during the week The code that generated the report (which I’ve used heavily and written about before) … Continue reading →

Idle thoughts lead to R internals: how to count function arguments

“Some R functions have an awful lot of arguments”, you think to yourself. “I wonder which has the most?” It’s not an original thought: the same question as applied to the R base package is an exercise in the Functions chapter of the excellent Advanced R. Much of the … Continue reading →

PubMed retractions report has moved

A brief message for anyone who uses my PubMed retractions report. It’s no longer available at RPubs; instead, you will find it here at Github. Github pages hosting is great, once you figure out that docs/ corresponds to your web root :) Now I really must update the code and try to make it … Continue reading →

Moving from RPubs to Github documents

If you still follow my Twitter feed – I pity you, as it’s been rather boring of late. Consisting largely of Github commit messages, many including the words “knit to github document”. Here’s why. RPubs, an early offering from RStudio, has been a great platform for easy … Continue reading →

Farewell then, PubMed Commons

PubMed Commons, the NCBI’s experiment in comments for PubMed articles, has been discontinued. Thoroughly too, with all traces of it expunged from the NCBI website. Last time I wrote about the service, I concluded “all it needs now is more active users, more comments per user and a real … Continue reading →

Twitter coverage of the Australian Bioinformatics & Computational Biology Society Conference 2017

You know the drill by now. Grab the tweets. Generate the report using RMarkdown. Push to Github. Publish to RPubs. This time it’s the Australian Bioinformatics & Computational Biology Society Conference 2017, including the COMBINE symposium. Looks like a good time was had by all in … Continue reading →

Mapping data using R and leaflet

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 article at ABC News. … Continue reading →

XML parsing made easy: is that podcast getting longer?

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 … Continue reading →

Feels like a dry winter – but what does the data say?

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 … Continue reading →

Infographic-style charts using the R waffle package

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 … Continue reading →

Years as coloured bars

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 trends within … Continue reading →