Introduction Requirements Set-up Why are you calling it a LAN party? Docker, containers, images TLDR: You can teach R on people’s own laptops without having them install anything or require an internet connection.
Members of the Surgical Informatics team in Ghana, 2019. More information: surgicalinformatics.org
Introduction Running R programming courses on people’s own laptops is a pain, especially as we use a lot of very useful extensions that actually make learning and using R much easier and more fun.
TLDR: there are two new and very intuitive R functions for reshaping data: see Examples of pivot_longer() and pivot_wider() below. At the time of writing, these new functions are extremely fresh and only exist in the development version on GitHub (see Installation), we should probably wait for the tidyverse team to officially release them (in CRAN) before putting them into day-to-day use.
Introduction The juxtapose of data collection vs data analysis: data that was very easy to collect, is probably very hard to analyse, and vice versa.
This post demonstrates the use of two very cool R packages - ggrepel and patchwork.
ggrepel deals with overlapping text labels (Code#1 at the bottom of this post):
patchwork is a very convenient new package for combining multiple different plots together (i.e. what we usually to use grid and gridExtra for).
To really demonstrate the power of them, let’s make a global map of country names using ggrepel:
I’ve been doing data science for over 10 years now. Although most of this time I didn’t realise I was doing data science. I thought I was just doing normal science but focusing on simulations and data analysis, rather than field or lab work. I’ve switched fields a few times now- physics BSc, Chemistry PhD, now working in medical research. Therefore, instead of this lenghty introduction:
“I’m a physicist by background with substantial interdisciplinary expertise in simulations, data analysis, programming…”
Day 0 (Sunday 18-February 2018) Left Edinburgh at 8am for a 1pm ferry Kennacraig to Port Askaig (Islay). Edinburgh-Kennacraig should be a 3.5h drive (and it was), but we left early to allow for any delays on the road. Arrived on Islay at 3pm and our accommodation near Port Ellen (southern Islay, close to to Ardbeg, Lagavulin, Laphroiaig) was a 40 min drive from the port.
Map of Islay with all its lovely distilleries.
Between 2014-2018 I published 29 posts on riinudata.wordpress.com. Today I’m converting all of those to my new website powered by blogdown-Hugo.
Step 1 Read the Migration: From Wordpress chapter of the blogdown book.
Step 2 Get all your wordpress posts into one XML: WP Admin - Tools - Export.
Step 3 Install Exitwp and its dependencies (pyyamp, beautifulsoup4, html2text):
git clone https://github.com/thomasf/exitwp.git sudo easy_install pip sudo pip install pyyaml sudo pip install beautifulsoup4 sudo pip install html2text This worked on macOS1 High Sierra - I already had python installed.
We are live! I wrote my last blog post on Wordpress on 20-October 2017 and promised myself this was the last time. I’ve been blogging on Wordpress since 2014 and the more I used it the more painful it got! This is most likely caused by the fact that I have been thrifting further and further away from point-and-click interfaces anyway…oh and discovering MARKDOWN.
My two rules: text is written in Markdown (I use R Markdown/knitr/bookdown, e.
I am completely obsessed with Shiny and these days I end up presenting most of my work in a Shiny app.
If it’s not worth putting in a Shiny app it’s not worth doing.
With a simple combination of mutate_if and fct_explicit_na,you can replace all NAs in all factors with “Missing”:
dplyr reference: http://dplyr.tidyverse.org/reference
forcats reference: http://dplyr.tidyverse.org/reference
To create a .bib file that only includes the citations you used in the manuscript:
bibexport -o extracted_file.bib manuscript.aux
There are a few issues with this though. The command bibexport comes with the installation of TexLive, but my Windows computer (bless) does not cooperate (“bibexport is not recognised as an internal or external command…”) . So I can only use it on my Mac (luv ya).