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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 maps of your study sites. It was written with the specific purpose of generating simple, clean figures for publications and presentations, which it achieves very nicely. I’ll be honest: the sole motivator for this post is that I thought it would be fun to generate the map using Leaflet for R as an alterna...
Source: What You're Doing Is Rather Desperate - July 17, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics leaflet maps rstats Source Type: blogs

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. A few changes required compared with previous reports, due to changes in the rtweet package, and a weird issue with kable tables breaking markdown headers. I love that the most popular media attachment is a screenshot of a Github repo. (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - July 16, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics rstats twitter user2018 Source Type: blogs

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 there. There are lots of R packages. We’ll limit ourselves to those packages which ship with R, and which load on startup. Which ones are they? What packages load on starting R? Start a new R session and type search(). Here’s the result on my machine: search() [1] ".GlobalEnv" "...
Source: What You're Doing Is Rather Desperate - June 21, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics Source Type: blogs

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 more interesting than a bunch of bar charts. (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - May 23, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics github pmretract pubmed retraction rstats Source Type: blogs

50% bananas
Today in “blog posts that have spent two years in the draft folder” – “Humans are 50% banana.” “Humans are 50% banana.” Perhaps you have heard this statement, or one like it. It seems to be widely-quoted. As an example it’s hard to go past this article from UK tabloid The Mirror which, in addition to the banana, also informs us that “the entire internet weighs about the same as one large strawberry”. I don’t even know where to begin with that one. A couple of years ago whilst between jobs and with time on my hands, I thought I’d go in search of the sou...
Source: What You're Doing Is Rather Desperate - May 9, 2018 Category: Bioinformatics Authors: nsaunders Tags: genomics humour banana human myths Source Type: blogs

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 and free publishing of HTML documents generated from RMarkdown and written in RStudio. That said, it’s always been very basic (e.g. no way to organise documents by content, tags). There’s been no real development of the platform for several years and of late, I’ve noticed it’s become less reliable. Bugs, ...
Source: What You're Doing Is Rather Desperate - April 4, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics this blog github markdown publlishing reports rpubs Source Type: blogs

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. Result: “NIH has decided that the low level of participation does not warrant continued investment in the project, particularly given the availability of other commenting venues.” NLM also write that “all comments are archived on our FTP site.” A CSV file is avail...
Source: What You're Doing Is Rather Desperate - March 15, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics comments pubmed commons rstats Source Type: blogs

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, the rtweet package went through a brief phase of returning lists instead of nice data frames. I hope that’s been discarded as a bad idea :) Second, results returned from a hashtag search that did not contain said hashtags, but were definitely from the meeting. Yet to get to th...
Source: What You're Doing Is Rather Desperate - November 20, 2017 Category: Bioinformatics Authors: nsaunders Tags: australia bioinformatics meetings statistics abacbs twitter Source Type: blogs

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 table containing Australian members of parliament, their electorate and their voting intention regarding legalisation of same-sex marriage. Since I reside in New South Wales, let’s map the data for electorates in that state. Here’s the code at Github. The procedure is pretty straightforward: Obtain a...
Source: What You're Doing Is Rather Desperate - November 14, 2017 Category: Bioinformatics Authors: nsaunders Tags: australia australian news statistics leaflet maps politics ssm Source Type: blogs

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 takes up about 10 hours of my week, so I found it hard to justify two hours for one podcast, no matter how good. Were the episodes really getting longer over time? Let’s find out using R. One thing I’ve learned as a data scientist: management want to see the key points first. So here it is: T...
Source: What You're Doing Is Rather Desperate - October 12, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics parsing podcast rss twiv xml Source Type: blogs

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 weeks or months at a time. The realisation hits slowly: at some point you look around at the yellow-brown lawns, ovals and “nature strips” and say “gee, I don’t remember the last time it rained.” Thankfully in our data-rich world, it’s relatively easy to find out whether the dry spell is really ...
Source: What You're Doing Is Rather Desperate - October 11, 2017 Category: Bioinformatics Authors: nsaunders Tags: australia statistics ggplot2 rainfall sydney underground weather Source Type: blogs

Infographic-style charts using the R waffle package
Conclusion That’s it, more or less. Are the icons any more effective than the squares? In certain settings, perhaps. You be the judge.Filed under: R, statistics Tagged: packages, rstats, visualization, waffle (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - September 8, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics packages rstats visualization waffle Source Type: blogs

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 categories over time – but I don’t think years as coloured bars is the way to go. To me, progression over time suggests that time should be an axis, so as the eye moves along the data from one end to the other, without interruption. What I want to see is categories over time, not time within categories. So what is the way to g...
Source: What You're Doing Is Rather Desperate - August 5, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics ggplot2 visualisation Source Type: blogs

To do analysis stuff
First there was “insert statistical method here“. Now we have R – making it easy “to do analysis stuff“. Via Elisabeth; I’ll hand you over now for an entertaining summary. To be fair, analysis stuff describes my working life quite well.  Filed under: humour, publications, uncategorized (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - August 2, 2017 Category: Bioinformatics Authors: nsaunders Tags: humour publications Source Type: blogs

Twitter Coverage of the ISMB/ECCB Conference 2017
Search all the hashtags 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 Brisbane 2003 (very enjoyable early in my bioinformatics career, but unfortunately the seed for the “no more southern hemisphere meetings” decision), and in Toronto 2008. The latter was notable for its online coverage and for me, the pleasure of...
Source: What You're Doing Is Rather Desperate - August 2, 2017 Category: Bioinformatics Authors: nsaunders Tags: bioinformatics meetings statistics eccb ismb twitter Source Type: blogs