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, for example, such as one document overwriting another when published from RStudio.

I think it’s unlikely that issues will be addressed, given that RStudio are now focused on RStudio Connect. So I’ve removed as many documents as I can and rewritten them as Github documents. These render as HTML when pushed to Github, generating attractive reports. Here’s an example.

I’ve done my best to update all blog posts here with links to the new reports. If you do come across old broken links to RPubs reports, just remember that the content is probably now at Github.

I’ve left a small number of reports at RPubs for now – those ones are interactive and use Javascript-based libraries such as Highcharter or Leaflet.

Taking steps (in XML)

So the votes are in:

I thank you, kind readers. So here’s the plan: (1) keep blogging here as frequently as possible (perhaps monthly), (2) on more general “how to do cool stuff with data and R” topics, (3) which may still include biology from time to time. Sounds OK? Good.

So: let’s use R to analyse data from the iOS Health app.

Read the rest…

Hiatus, indefinite

May. No blog posts yet in 2016. “What’s going on Neil?” asked no-one at all. For anyone who may be wondering…

Last November, I resigned from my position with my previous employer after almost 7 years. Just before Christmas, I was offered a position as a data scientist with a Sydney-based healthcare technology start-up. I started working there in early January and so far, it has been a terrific experience. Had I known how enjoyable it could be, I would have made a move like this 10 years ago. Career advice: there are many more jobs that can engage scientists and utilise their skills than academic research.

So what does that mean for this blog? It means that I’m no longer a researcher, at least in the narrow sense that science would use that word. It means that the things I learn during a working day are unlikely to translate into blog posts of broader interest (confidentiality issues not withstanding). And quite frankly, given where I’m at in my life (balancing working for a startup with raising my family), it means that I no longer have time to write regular blog posts.

Like a band that never officially breaks up, I’m not ready to declare the end just yet. So I’m placing the blog “on hiatus”, indefinitely. I’ll still be active online, which right now mostly means Twitter.

This blog in 2015

It must be time for the annual report, kindly generated by the people from WordPress at the end of each year.

I’m pleased to see that I still averaged almost 2 posts a month, given that it was a difficult year in many ways (more on that later). Visitors from 202 countries! And if I never blogged again, it seems that people will want to learn about R’s apply functions for a long time to come.

2016 is going to be a bit “different”. Look out for the blog post which explains how and why, coming soon…

A minor update to my “apply functions” post

One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not.

So: thanks to BioStar user zx8754 for pointing me to this Stack Overflow post, in which someone complains that the code in the post does not work as described. The by example is now fixed.

Side note: I often find “contact the author” is the most direct approach to solving this kind of problem ;) always happy to be contacted.

This blog in 2013

In something of an end-of-year tradition, WordPress provides users with an effort-free blog post in the form of an annual report. Here is mine.

My ambitious plan at the start of 2013 was to aim for 4 posts a month. I managed 28 and I’m happy with that; about one every two weeks.

Looking forward to a new year of blogging. All the best to you and yours for 2014.

This blog: 2012 in review

Thankfully, have established an end-of-year tradition whereby you get a blog post for no effort, in the form of an annual report. Here it is.

Frankly, I’m amazed that I managed even 22 posts – hey, that’s almost 1 every 2 weeks! As for 2013…no promises. However, I’m looking forward to sharing at least a few useful snippets with you. All the best to you and yours for the coming year.

Draft post cull

Work and life are currently impacting the frequency of my blogging. I’m falling back on the old trick of clearing out draft posts and explaining briefly why they never saw the light of day.

1. How to launch a website (January 18, 2012)
Anyone can publish a website. Is this a good thing? In one sense yes, of course – empowerment and democratization of information are important. However, I’m increasingly of the opinion that scientific websites should meet some minimum standards and that those who create them have an appropriate level of programming competency. Having an idea is great but if it’s poorly-implemented, tools will break, whither and die, creating a Web of broken links and non-functional resources.

So the title of this post was supposed to be ironic and it went on to list a series of steps which described (wittily I hoped) how not to launch a website. Unfortunately, when I read over the post, it was not at all witty. In fact, it was just a thinly-veiled attack on a recently launched aggregator.

I think some of the points in the post do need to be made, but not in their current form and perhaps not by me.

2. Google Plus: what’s in it for the online scientist? (July 1, 2011)
I started to write this one when Google+ first launched. There were more than enough posts which reviewed its features so, as the title suggests, I was trying to come up with a different angle: how useful might G+ be for scientists?

In the end, I simply could not come up with anything interesting to say. I know that other scientists use G+ and find it very useful. I’m not one of them – in fact, I don’t use it at all. What’s more, I can’t even explain why. It’s not that I have strong feelings one way or the other about G+; for some reason, it just doesn’t register on my “must investigate” radar.

Still to come (hopefully)

1. Sequencing for relics from the Sanger era part 2: FASTQ manipulation and sequence quality
There are supposed to be 4 posts in my NGS series and this one looks at tools for manipulation and QC of FASTQ sequence files. My NGS self-education is a side-project and “real work” takes precedence just now, so no timeline promises for this one. Soon, I hope.

2. My day out at #osddmalaria
I’ve been meaning to write a summary of my day at the Open Source Drug Discovery Malaria meeting, back in February. Here’s a brief one: it was really interesting and I enjoyed it. More than that to follow at some point.