Blog Archives

An update to the nhmrcData R package

March 15, 2017
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An update to the nhmrcData R package

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 … Continue...

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The nhmrcData package: NHMRC funding outcomes data made tidy

March 8, 2017
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The nhmrcData package: NHMRC funding outcomes data made tidy

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 package (more correctly, R data … Continue...

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HTML vignettes crashing your RStudio? This may be the reason

March 5, 2017
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HTML vignettes crashing your RStudio? This may be the reason

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 installed version of rmarkdown (1.3 in my … Continue...

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Twitter Coverage of the Lorne Genome Conference 2017

February 16, 2017
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Twitter Coverage of the Lorne Genome Conference 2017

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’s project then: use R to analyse … Continue...

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Hyetographs, hydrographs and highcharter

February 6, 2017
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Hyetographs, hydrographs and highcharter

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 “rainfall hyetograph and streamflow hydrograph”, which … Continue...

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Nice graphic? Are they taking the p…

February 4, 2017
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Nice graphic? Are they taking the p…

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). And third…do I have to spell this out…those are 3D … Continue...

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The real meaning of spurious correlations

February 2, 2017
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The real meaning of spurious correlations

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 is, however, a more formal definition of … Continue...

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Taking steps (in XML)

February 1, 2017
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Taking steps (in XML)

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 monthly), (2) … Continue...

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Evidence for a limit to effective peer review

December 18, 2016
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Evidence for a limit to effective peer review

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 fact-check article from Dutch news organisation NRC titled “Nature

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An Analysis of Contributions to PubMed Commons

December 1, 2016
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An Analysis of Contributions to PubMed Commons

I recently saw a tweet floating by which included a link to some recent statistics from PubMed Commons, the NCBI service for commenting on scientific articles in PubMed. Perhaps it was this post at their blog. So I thought now would be a good time to write some code to analyse PubMed Commons data. The

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