Monthly Archives: December 2016

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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How to build a Shiny app for disease- & trait-associated locations of the human genome

December 17, 2016
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This app is based on the gwascat R package and its ebicat38 database and shows trait-associated SNP locations of the human genome. You can visualize and compare the genomic locations of up to 8 traits simultaneously. The National Human Genome Research...

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help(let, package=’replyr’)

December 17, 2016
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A bit more on our replyr R package. library("replyr") help(let, package='replyr') let {replyr} R Documentation Prepare expr for execution with name substitutions specified in alias. Description replyr::let implements a mapping from desired names (names used directly in the expr code) to names used in the data. Mnemonic: "expr code symbols are on the left, external … Continue...

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Air quality in Indian cities

December 17, 2016
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Air quality in Indian cities

Seasonal air pollution in India The motivation for this blog post was a conference paper I recently heard that analysed five years of daily pollution data in an India city with a non-seasonal auto-regressive integrated moving average (ARIMA) model. In discussion after the presentation, there were differing views on whether such data should be modelled with a seasonal approach,...

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Learning how to extend #RStudio by reading books

December 17, 2016
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Learning how to extend #RStudio by reading books

This post is part of a series of "learning everything with R: An R book list". You can clink on this link to see other relevant posts. RStudio probably is the most popular interface to use R. But it definitely does not just serve as a code editor (than...

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ggtree version of plotTree

December 16, 2016
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ggtree version of plotTree

PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc. I reproduced the examples presented in the plotTree repo using ggtree. Source code is...

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A Political Cartoon and a Markov Chain

December 16, 2016
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A Political Cartoon and a Markov Chain

Pat Bagley is easily my favorite political cartoonist, period. For the politically aware in Utah, he is almost legendary, enjoying superstar status. I’ve been aware of him since I was a kid, and I always loved his cartoons. Not only does his artistic style appeal to me, he has a way of illustrating a situation…Read more A...

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Automatically generated join-the-dots images

December 16, 2016
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Automatically generated join-the-dots images

It is interesting to try and figure out what picture emerges from a join-the-dots puzzle (connect-the-dots in some parts of the world). Let’s have a go at some lightweight automatic generation such a puzzle (some heavy-weight techniques). If an image is available, expressed as an boolean matrix, R’s sample function can be used to select

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Reproducible Finance with R: A Shiny ETF Map

December 16, 2016
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by Jonathan Regenstein In a previous post, we built an R Notebook that laid the groundwork for a Shiny app that allows users to graph country ETFs by clicking on a world map. In today’s Fun Friday post, we’ll charge forth to build that app, again using a flexdashboard so that we can stay in

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Predicting flu deaths with R

December 16, 2016
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Predicting flu deaths with R

As Google learned, predicting the spread of influenza, even with mountains of data, is notoriously difficult. Nonetheless, bioinformatician and R user Shirin Glander has created a two-part tutorial about predicting flu deaths with R (part 2 here). The analysis is based on just 136 cases of influenza A H7N9 in China in 2013 (data provided in the outbreaks package)...

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