Blog Archives

Just use a scatterplot. Also, Sydney sprawls.

July 17, 2018
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Just use a scatterplot. Also, Sydney sprawls.

Sydney’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 cities that are low density, but have comparable average commute times to higher-density cities. … Continue reading Just...

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Using leaflet, just because

July 17, 2018
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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 of these is Making … Continue reading Using...

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Twitter coverage of the useR! 2018 conference

July 16, 2018
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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) is at Github too. … Continue reading Twitter...

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

June 21, 2018
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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 information in this post came from … Continue reading Idle...

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PubMed retractions report has moved

May 22, 2018
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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 more … Continue reading PubMed...

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Moving from RPubs to Github documents

April 4, 2018
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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 and free publishing of HTML documents generated from … Continue reading Moving...

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Farewell then, PubMed Commons

March 14, 2018
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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 API.” None of those things happened. … Continue reading Farewell...

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

November 20, 2017
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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 Adelaide. A couple of quirks this time around. First, … Continue reading Twitter...

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Mapping data using R and leaflet

November 14, 2017
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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. It includes a … Continue reading Mapping...

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XML parsing made easy: is that podcast getting longer?

October 12, 2017
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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 commuting to/from work, which … Continue reading XML...

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