Decision Mechanics

Insight. Applied.

COVID-19 epidemiology with R

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Interesting, and timely, article on using R to analyse COVID-19 incidence data collated by John Hopkins University.

It makes use of two epidemiology packages.

  • earlyR for estimation of infectiousness, as measured by the reproduction number (R), in the early stages of an outbreak.

  • EpiEstim for estimating the time varying instantaneous reproduction number during epidemics

These packages, and many more, are part of the R Epidemics Consortium (RECON). They

[…] gather experts in data science, modelling methodology, public health, and software development to create the next generation of analytics tools for informing the response to disease outbreaks, health emergencies and humanitarian crises, using the R software and other free, open-source resources.

Pandas in 8 pages

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Pandas is a Python package for working with tabular data—as in a spreadsheet or database table. It provides similar functionality to R’s data frames.

As pandas is rich in features it can be difficult to remember all its operations and syntax, so Enthought have produced a visual guide to the package in 8 handy pages.

Is it easier to learn R or Python?

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Andy Kirk at Visualising Data ran a Twitter poll about the relative accessibility of R and Python to non-developers.

59% said that R was more accessible.

Obviously, the poll is far from scientific, but the comments he received reflect my own experiences of teaching both languages—such as the significance of the RStudio IDE and the tidyverse packages in getting people off the ground.

BBC News using ggplot2 for production-ready charts

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Chart montage

BBC News are using the R ggplot2 package to create production-ready charts—which illustrates the flexibility and power of this package.

What’s particularly interesting is the approach they’ve taken to training their staff to use R. Initiatives include

  • sharing of tricks and tips through a living cookbook (knowledge base)

  • a six week course comprising six short introductions with links to online resources

  • a dedicated Slack channel for course participants to discuss issues or ask for help

  • an end-of-course project/challenge that exercises the skills developed over the six weeks

The strategies of spreading training over an extended period and embedding it in the workplace have been shown to increase retention and assist in moving from learning to delivering value to the business.