Jane Frazier spoke at our research team meeting today on “Reproducibility in computational research”. We had a very stimulating and lively discussion about the issues involved. One interesting idea was that reproducibility is on a scale, and we can all aim to move further along the scale towards making our own research more reproducible. For […]
Reproducibility is hard. It will probably always be hard, because it’s hard keeping things organized. I recently had a paper accepted at G3, concerning a huge set of sample mix-ups in a large eQTL study. I’d discovered and worked out the issue back in December, 2010. I gave a talk about it at the Mouse […]
Reproducibility is hard. It will probably always be hard, because it’s hard keeping things organized. I recently had a paper accepted at G3, concerning a huge set of sample mix-ups in a large eQTL study. I’d discovered and worked out the issue back in December, 2010. I gave a talk about it at the Mouse […]
There are some tools that I use regularly, and I would like my research students and post-docs to learn them too. Here are some great online tutorials that might help. ggplot tutorial from Winston Chang Writing an R package from Karl Broman Rmarkdown from RStudio Shiny from RStudio git/github guide from Karl Broman minimal make tutorial from Karl […]
Every now and then a commercial software vendor makes claims on social media about how their software is so much better than the forecast package for R, but no details are provided. There are lots of reasons why you might select a particular software solution, and R isn’t for everyone. But anyone claiming superiority should […]
Yahoo Labs has just released an interesting new data set useful for research on detecting anomalies (or outliers) in time series data. There are many contexts in which anomaly detection is important. For Yahoo, the main use case is in detecting unusual traffic on Yahoo servers. The data set comprises real traffic to Yahoo services, along […]
In anticipation of next week’s Reproducible Science Hackathon at NESCent, I was thinking about Christie Bahlai’s post on “Baby steps for the open-curious.” Moving from Ye Olde Standard Computational Science Practice to a fully reproducible workflow seems a monumental task, but partially reproducible is better than not-at-all reproducible, and it’d be good to give people […]
The Human Mortality Database is a wonderful resource for anyone interested in demographic data. It is a carefully curated collection of high quality deaths and population data from 37 countries, all in a consistent format with consistent definitions. I have used it many times and never cease to be amazed at the care taken to maintain […]
Hadley Wickham is writing what will surely be a great book about the basics of R packages. And Hilary Parker wrote a very influential post on how to write an R package. So it seems like that topic is well covered. Nevertheless, I’d been thinking for some time that I should write another minimal tutorial […]
![implementing reproducible research [short book review]](http://images.tandf.co.uk/common/jackets/crclarge/978146656/9781466561595.jpg)
As promised, I got back to this book, Implementing reproducible research (after the pigeons had their say). I looked at it this morning while monitoring my students taking their last-chance R exam (definitely last chance as my undergraduate R course is not reconoduced next year). The book is in fact an edited collection of papers […]
