https://riinu.me/ Recent content on Riinu's scripting diary Hugo -- gohugo.io en-us Mon, 11 Aug 2025 00:00:00 +0000 https://riinu.me/2025/08/accuracy/ Mon, 11 Aug 2025 00:00:00 +0000 https://riinu.me/2025/08/accuracy/ TLDR: The terms precision and accuracy should not be used interchangeably, as it is possible to be precisely wrong or roughly right. Not precise, but accurate is also known as roughly right - Figure (a). Not accurate, but precise is also known as precisely wrong - Figure (d). Being accurate means your estimates or measurements are close to ground truth. Determining accuracy can only be done via validation or calibration. https://riinu.me/2025/07/dpi/ Fri, 04 Jul 2025 00:00:00 +0000 https://riinu.me/2025/07/dpi/ TLDR: For high quality images in HTML and Word outputs change your DPI setting to 200 or 300. The default DPI of figures created by R Markdown or Quarto for HTML and Word outputs is 96 (dots per inch - resolution). This may be sufficient for web purposes (HTML), but not sufficient for publishing manuscripts (Word). PDFs include vector graphics and are therefore infinite resolution. In R Markdown, DPI can be changed in the set-up chunk, by including knitr::opts_chunk$set(dpi = 300) in the set-up chunk: https://riinu.me/2024/02/consort/ Fri, 02 Feb 2024 00:00:00 +0000 https://riinu.me/2024/02/consort/ TLDR: library(consort) is a great package for creating CONSORT/patient flow diagrams in R. Thank you author Alim Dayim! Jump to example code. Documentation. Introduction The easiest way to make a one-off diagram is using something with a graphical interface, such as Power Point, Omnigraffle, or Lucidchart, just to name a few. If, however, you need something that updates automatically based on the underlying dataset changing, then a programmatical solution using R is possible. https://riinu.me/2023/08/quarto/ Sun, 27 Aug 2023 00:00:00 +0000 https://riinu.me/2023/08/quarto/ What is Quarto? Prerequisites 1. Create a new Quarto website project Troubleshooting 2. Edit your Quarto website 3. Add a page to your website 4. Add R code to your website 5. Serve your website using Netlify Optional: If want to keep the site for longer than 1h 6. Update your website Optional advanced: automatic deploys via GitHub I’ve put together a quick ‘getting started with Quarto and Netlify and GitHub (optional) workshop’. https://riinu.me/2023/08/healthyr-advent/ Sun, 27 Aug 2023 00:00:00 +0000 https://riinu.me/2023/08/healthyr-advent/ The HealthyR Advent Calendar 2022 was a series of 24 R tips I shared on Twitter last December It is based on “R for Health Data Science” by Harrison and Pius. Use JKL20 for 20% off, including free worldwide shipping. Here’s a selection of the most popular ones, all 24 can be fount at this website: https://healthyradvent.netlify.app/ More information about HealthyR, including the book and freely available resources can be found at: https://healthyr. https://riinu.me/2022/02/world-map-ggplot2/ Fri, 25 Feb 2022 00:00:00 +0000 https://riinu.me/2022/02/world-map-ggplot2/ There are several different ways to make maps in R, and I always have to look it up and figure this out again from previous examples that I’ve used. Today I had another look at what’s currently possible and what’s an easy way of making a world map in ggplot2 that doesn’t require fetching data from various places. TLDR: Copy this code to plot a world map using the tidyverse: https://riinu.me/2022/01/wide-to-long-multiple/ Fri, 28 Jan 2022 00:00:00 +0000 https://riinu.me/2022/01/wide-to-long-multiple/ There’s some explanation on what reshaping data in R means, why we do it, as well as the history, e.g., melt() vs gather() vs pivot_longer() in a previous post: New intuitive ways for reshaping data in R That post shows how to reshape a single variable that had been recorded/entered across multiple different columns. But if multiple different variables are recorded over multiple different columns, then this is what you might want to do: https://riinu.me/2021/09/create-website/ Fri, 24 Sep 2021 00:00:00 +0000 https://riinu.me/2021/09/create-website/ I’ve just set up a single page website (= online business card) for myself and my husband: https://pius.cloud/ . This post summarises what I did. If you’re looking to get started with something super quickly, then only the first two steps are essential (Creating a website and Serving a website). Creating a website (using Nicepage) I’ve created websites using various tools such as straight up HTML, Wordpress, Hugo+blogdown (this site - riinu. https://riinu.me/2020/02/r-filtering-with-na-values/ Thu, 27 Feb 2020 00:00:00 +0000 https://riinu.me/2020/02/r-filtering-with-na-values/ NA - Not Available/Not applicable is R’s way of denoting empty or missing values. When doing comparisons - such as equal to, greater than, etc. - extra care and thought needs to go into how missing values (NAs) are handled. More explanations about this can be found in the Chapter 2: R basics of our book that is freely available at the HealthyR website This post lists a couple of different ways of keeping or discarding rows based on how important the variables with missing values are to you. https://riinu.me/2019/11/rstudio-server-lan-party/ Fri, 15 Nov 2019 00:00:00 +0000 https://riinu.me/2019/11/rstudio-server-lan-party/ 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. But long installation instructions can be very off-putting for complete beginners, and people can be discouraged to learn programming if installation hurdles invoke their imposter syndrome. https://riinu.me/2019/04/new-intuitive-ways-to-reshape-data-in-r/ Sun, 07 Apr 2019 00:00:00 +0000 https://riinu.me/2019/04/new-intuitive-ways-to-reshape-data-in-r/ 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. Exciting! 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. https://riinu.me/2018/09/global-map-of-country-names/ Sun, 16 Sep 2018 00:00:00 +0000 https://riinu.me/2018/09/global-map-of-country-names/ 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). More info: https://github.com/slowkow/ggrepel https://github.com/thomasp85/patchwork To really demonstrate the power of them, let’s make a global map of country names using ggrepel: https://riinu.me/2018/04/islay-distilleries-in-3-days/ Sun, 01 Apr 2018 00:00:00 +0000 https://riinu.me/2018/04/islay-distilleries-in-3-days/ 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. https://riinu.me/2018/02/converting-old-wordpress-posts-to-hugo/ Sat, 24 Feb 2018 00:00:00 +0000 https://riinu.me/2018/02/converting-old-wordpress-posts-to-hugo/ 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. https://riinu.me/2018/02/hello-world/ Mon, 12 Feb 2018 00:00:00 +0000 https://riinu.me/2018/02/hello-world/ 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. https://riinu.me/2017/10/your-first-shiny-app/ Fri, 20 Oct 2017 00:00:00 +0000 https://riinu.me/2017/10/your-first-shiny-app/ What is Shiny? Shiny is an R package (install.packages("shiny")) for making your outputs interactive. Furthermore, Shiny creates web apps meaning your work can be shared online with people who don’t use R. In other words: with Shiny, R people can make websites without ever learning Javascript etc. 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. https://riinu.me/2017/07/r-replacing-nas-in-all-factors-with-missing/ Wed, 19 Jul 2017 00:00:00 +0000 https://riinu.me/2017/07/r-replacing-nas-in-all-factors-with-missing/ 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 https://riinu.me/2017/06/handling-your-bib-file-latex-bibliography/ Sat, 17 Jun 2017 00:00:00 +0000 https://riinu.me/2017/06/handling-your-bib-file-latex-bibliography/ 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). https://riinu.me/2016/12/get-data-from-ggplot/ Tue, 06 Dec 2016 00:00:00 +0000 https://riinu.me/2016/12/get-data-from-ggplot/ ggplot includes built in and seamless functionality that summarises your data before plotting it. As shown in the example below, ggplot_build() can be used to access the summarised dataset. fill y count prop x PANEL group ... #D7301F 0.2147239 35 1 1 1 4 ... #FC8D59 0.6871166 77 1 1 1 3 ... #FDCC8A 0.9570552 44 1 1 1 2 ... #FEF0D9 1.0000000 7 1 1 1 1 ... #D7301F 0. https://riinu.me/2016/10/r-lingua-library-vs-package/ Mon, 10 Oct 2016 00:00:00 +0000 https://riinu.me/2016/10/r-lingua-library-vs-package/ https://riinu.me/2016/09/online-syntax-highlighter/ Mon, 26 Sep 2016 00:00:00 +0000 https://riinu.me/2016/09/online-syntax-highlighter/ http://markup.su/highlighter/ The style I use: Dawn https://riinu.me/2016/09/r-iso-codes-and-country-names/ Mon, 26 Sep 2016 00:00:00 +0000 https://riinu.me/2016/09/r-iso-codes-and-country-names/ install.packages(‘maps’) iso = maps::iso3166 > str(iso) 'data.frame': 269 obs. of 5 variables: $ a2 : chr "AW" ... $ a3 : chr "ABW" ... $ ISOname : chr "Aruba" .. $ mapname : chr "Aruba" ... $ sovereignty: chr "Netherlands" ... https://riinu.me/2016/07/adding-a-cron-job-using-the-ed-editor/ Mon, 25 Jul 2016 00:00:00 +0000 https://riinu.me/2016/07/adding-a-cron-job-using-the-ed-editor/ These commands (after the first one) work in the ed editor. ed editor is used in the RStudio server shell. sudo crontab -e #opens crontab file in chosen editor a #add to file 0,30 * * * * Rscript /home/user/folder/script.R #command to add . #finished editing ,p #print file content to check w #save changes Q #quit In this example the script will run every 0 hours, 30 minutes, see Ubuntu: How do I set up a CRON job for other options. https://riinu.me/2016/04/add-abcd-labels-on-ggplot-facets/ Sun, 17 Apr 2016 00:00:00 +0000 https://riinu.me/2016/04/add-abcd-labels-on-ggplot-facets/ https://riinu.me/2016/04/how-long-did-my-script-run/ Fri, 15 Apr 2016 00:00:00 +0000 https://riinu.me/2016/04/how-long-did-my-script-run/ This to the beginning: strt<-Sys.time() And this to the end: print(Sys.time()-strt) Example output: print(Sys.time()-strt) Time difference of 16.39691 secs https://riinu.me/2016/04/adding-space-between-rows-in-latex-tables/ Mon, 11 Apr 2016 00:00:00 +0000 https://riinu.me/2016/04/adding-space-between-rows-in-latex-tables/ By default, LaTex tables are very tight: \usepackage{booktabs} \begin{table}[] \centering \caption{My caption} \label{my-label} \begin{tabular}{@{}lll@{}} \toprule Rows & Column 1 & Column 2 \\ \midrule Row 1 & 1234 & 2345 \\ Row 2 & 3456 & 4567 \\ Row 3 & 5678 & 6789 \\ Row 4 & 7890 & 8901 \\ Row 5 & 9012 & 10000 \\ \bottomrule \end{tabular} \end{table} Adding this to the document preamble will add space between the rows: https://riinu.me/2016/03/my-minimal-latex-preamble/ Wed, 23 Mar 2016 00:00:00 +0000 https://riinu.me/2016/03/my-minimal-latex-preamble/ My minimal example: \documentclass[a4paper]{article} %%% FIGURES AND TABLES %%%% \usepackage{graphicx} %gives the \includegraphics[width=0.5\textwidth]{my_image} %%% PAGE AND TEXT SET-UP %%%% \usepackage{fullpage} %gets rids of the wide default borders \renewcommand{\baselinestretch}{1.5} %space between lines \begin{document} Hello hello hello \end{document} And then one that is not so minimal, but still pretty basic and useful: \documentclass[a4paper]{article} %%% FIGURES AND TABLES %%%% \usepackage{graphicx} %gives the \includegraphics[width=0.5\textwidth]{my_image} \usepackage{booktabs} %for nicer tables \usepackage{tabu} %advanced control over tables \renewcommand{\thetable}{S\arabic{table}} %if this is supplement (this numbers figures as S1, S2. https://riinu.me/2015/09/how-to-increase-array-resolution-in-r-replicate-each-element-both-column-wise-and-row-wise/ Sat, 12 Sep 2015 00:00:00 +0000 https://riinu.me/2015/09/how-to-increase-array-resolution-in-r-replicate-each-element-both-column-wise-and-row-wise/ One picture says more than a thousand words. You have what is one the left, and you want what is on the right. my_matrix = matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9), nrow=3) #matrix is a 2D array, this next row creates a third dimension, #duplicating the data my_array = array(my_matrix, dim = c(3,3,2)) There are a few different ways to do this, but by far the cleanest and quickest way is to just select the rows and columns multiple times, by replicating row and column numbers (instead of actually replicating each element): https://riinu.me/2015/06/cut-a-time-period-from-netcdf-with-nco/ Tue, 30 Jun 2015 00:00:00 +0000 https://riinu.me/2015/06/cut-a-time-period-from-netcdf-with-nco/ ncks -d time,start_time,end_time in.nc out.nc start_time and end_time are integers. Add -F, if you want to use Fortran indexing (to start from 1). No space between dimension name and start-end points! https://riinu.me/2015/06/converting-r-markdown-to-latex/ Wed, 24 Jun 2015 00:00:00 +0000 https://riinu.me/2015/06/converting-r-markdown-to-latex/ Install Pandoc: http://pandoc.org/ library(knitr) knit('report.Rmd') #This creates 'report.md' Open the Terminal, Command Prompt (search for cmd) or Windows Powershell, go to the folder and do: pandoc -s report.md -o report.tex And that’s it! (Read this, if you want vector images.) https://riinu.me/2015/06/reordering-factor-levels-in-r-and-what-could-go-wrong/ Thu, 11 Jun 2015 00:00:00 +0000 https://riinu.me/2015/06/reordering-factor-levels-in-r-and-what-could-go-wrong/ I’ve recently started using ggplot2 in addition to lattice (see this post that I made a while ago, explaining how I got into using lattice in the first place). Hint: when using ggplot2, you’ll need to use of the reshape2 package (also written by the amazing Hadley Wickham) to get your data into a form that ggplot2 works best with. Another thing that you’ll want to think about when using ggplo2 is factor levels. https://riinu.me/2014/11/latex-tables-column-widths-and-allignments/ Tue, 04 Nov 2014 00:00:00 +0000 https://riinu.me/2014/11/latex-tables-column-widths-and-allignments/ Firstly, start off your table in http://www.tablesgenerator.com/. Tables Generator will do a lot for you. Its most useful features are importing from .csv and merging cells. The Booktabs table style (alternative to default table style from the menu) looks a bit nicer and is “publication quality”. Note that publication quality tables should not contain vertical lines. Code #1 is the code from Tables Generator with the addition of caption, label and Latex document begin-end (so it’s compilable). https://riinu.me/2014/08/why-does-linear-model-without-an-intercept-forced-through-the-origin-have-a-higher-r-squared-value-calculated-by-r/ Wed, 06 Aug 2014 00:00:00 +0000 https://riinu.me/2014/08/why-does-linear-model-without-an-intercept-forced-through-the-origin-have-a-higher-r-squared-value-calculated-by-r/ This is a short note based on this. Answer in short: Because different formulas are used to calculate the R-squared of a linear regression, depending on whether it has an intercept or not. R2 for a linear model that has an intercept: , where y is the variable that the linear model is trying to predict (the response variable), y^ is the predicted value and y- is the mean value of the response variable. https://riinu.me/2014/07/rotate-with-imagemagick/ Wed, 23 Jul 2014 00:00:00 +0000 https://riinu.me/2014/07/rotate-with-imagemagick/ convert -rotate 270 -density 300 -compress lzw in.pdf out.pdf https://riinu.me/2014/07/how-to-temporarily-disable-a-bash-alias/ Tue, 22 Jul 2014 00:00:00 +0000 https://riinu.me/2014/07/how-to-temporarily-disable-a-bash-alias/ If you’ve defined alias ls='ls -al –color=auto', but want to use ls without the extra information and colouring then use \ls or equivalently command ls https://riinu.me/2014/07/symbolic-links-and-2-common-errors-with-them/ Tue, 22 Jul 2014 00:00:00 +0000 https://riinu.me/2014/07/symbolic-links-and-2-common-errors-with-them/ I don’t know if it’s good or bad, but I like when the files I’m working with are in the working directory (so instead of using pathnames to my files I can just type filename or ./filename). But to avoid copying data and wasting space, symbolic links are the way to go. The command for that is: ln -s target_file sym_link, where -s stands for “symbolic” (just ln would create a hard link) https://riinu.me/2014/05/add-up-the-values-of-two-variables-of-a-netcdf-file/ Thu, 29 May 2014 00:00:00 +0000 https://riinu.me/2014/05/add-up-the-values-of-two-variables-of-a-netcdf-file/ NCO:ncap2 is the function to do it: ncap2 -s 'new_var=var1+var2' in_filename.nc out_filename.nc The output file will have all of the variables that exist in the input file as well as the new_var. Add -O if your input and output files are the same (overwrite). I do not know what the -s stands for. BUT the new_var will have the same long_name as the first variable used for summing (i.e. it could make some things a bit confusing). https://riinu.me/2014/05/my-bash-aliases/ Thu, 29 May 2014 00:00:00 +0000 https://riinu.me/2014/05/my-bash-aliases/ If you find yourself using some commands always with the same flags, then it would make sense to define them as alieses, by putting them into your .bashrc file like this (log out and back in for it to take effect): # .bashrc # Put user specific aliases and functions here alias ls='ls -al --color=auto' alias qstat='qstat -a' alias qsub='qsub -m abe -M myemail@email.com' alias disk="du * -sh | sort -h" -a for ls shows hidden files (files that start with a dot, like . https://riinu.me/2014/05/saving-some-variables-from-a-netcdf-to-a-new-file/ Thu, 29 May 2014 00:00:00 +0000 https://riinu.me/2014/05/saving-some-variables-from-a-netcdf-to-a-new-file/ The NCO (netCDF Operator) command ncks (netCDF Kitchen Sink). From the documentation: The nickname “kitchen sink” is a catch-all because ncks combines most features of ncdump and nccopy with extra features to extract, hyperslab, multi-slab, sub-set, and translate into one versatile utility. ncks extracts (a subset of the) data from input-file and and writes (or pastes) it in netCDF format to output-file, and optionally writes it in flat binary format to binary-file, and optionally prints it to screen. https://riinu.me/2014/05/sum-all-values-over-several-dimensions-of-a-netcdf-variable/ Thu, 29 May 2014 00:00:00 +0000 https://riinu.me/2014/05/sum-all-values-over-several-dimensions-of-a-netcdf-variable/ NCO:ncap2 and .total ncap2 -s 'summed_variable=variable_to_sum.total($lat,$lon)' in.nc out.nc Make sure to use single quotes. If your in.nc==out.cnc then adding -A will save you from having to specify “overwrite” (see this). ncap2 -A -s 'summed_variable=variable_to_sum.total($lat,$lon)' in.nc out.nc