Slides for fifth session
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05_clean_coding/05_clean_coding.tex
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05_clean_coding/05_clean_coding.tex
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\documentclass[aspectratio=169]{beamer}
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\usepackage{listings}
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%\usepackage[utf8]{inputenc}
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\usepackage[style = apa, backend = biber, natbib = true]{biblatex}
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\addbibresource{../literature/lit.bib}
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\usepackage{fancyvrb}
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\usepackage{fontawesome5} % get icons
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\usepackage{multirow}
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\usepackage{color, colortbl}
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\usepackage{tikz}
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\usetikzlibrary{fit}
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\usepackage[edges]{forest}
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\lstset{language = R,%
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\newcommand{\gvect}[1]{\boldsymbol{#1}}
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\newcommand{\gmat}[1]{\boldsymbol{#1}}
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\AtBeginSection[]{
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\frame{
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\tableofcontents[sectionstyle=show/hide, subsectionstyle=show/show/hide]}}
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\setbeamertemplate{headline}{
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\begin{beamercolorbox}{section in head}
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\vskip5pt\insertsectionnavigationhorizontal{\paperwidth}{}{}\vskip2pt
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}
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\setbeamertemplate{footline}{\vskip-2pt\hfill\insertframenumber$\;$\vskip2pt}
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\title{Clean coding}
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\author{Nora Wickelmaier}
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\date{July 8, 2024}
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\begin{document}
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\begin{frame}{}
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\thispagestyle{empty}
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\titlepage
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\end{frame}
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\begin{frame}{What is needed to make code reproducible?}
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% slido
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\centering
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\includegraphics[width = 5cm]{../figures/QR Code for Methodenseminar SS 2024 - Session 5}
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\url{https://app.sli.do/event/uEz8fJWkLBNm1sthQovXNH}
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\end{frame}
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\begin{frame}[fragile]{Programming resources}
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\footnotesize
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\begin{tabular}{ll}
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Learning statistics with R & {\url{https://learningstatisticswithr.com/book/}} \\
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&\\
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R for Data Science & {\url{https://r4ds.hadley.nz/}} \\
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&\\
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Advanced R & {\url{https://adv-r.hadley.nz/}} \\
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&\\
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Happy Git and GitHub for the useR & {\url{https://happygitwithr.com/}} \\
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&\\
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R Programming for Research & {\url{https://geanders.github.io/RProgrammingForResearch/}} \\
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&\\
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Building reproducible analytical pipelines with R & {\url{https://raps-with-r.dev/}} \\
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&\\
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Data Skills for Reproducible Science & {\url{https://psyteachr.github.io/msc-data-skills/}} \\
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\end{tabular}
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\end{frame}
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\begin{frame}{Agenda}
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\centering
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\begin{tabular}{ll}
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\hline
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Date & Topic \\
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\hline
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2024-05-13 & Introduction to data management \\
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2024-05-27 & Workflow \\
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2024-06-10 & Data organisation\\
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2024-06-24 & Data sharing \\
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\only<1>{2024-07-08}\only<2>{\bf 2024-07-08} &
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\only<1>{Clean coding}\only<2>{\bf Clean coding} \\
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2024-07-22 & Version control \\
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\hline
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\end{tabular}
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\end{frame}
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% Understandable coding
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% Cleaning up R code for readability
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% Documentation of a final R script
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% Reproducible code
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\section{Style guidelines}
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\begin{frame}[<+->]{Style guidelines in R}
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\begin{itemize}
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\item R has no mandatory or commonly accepted style guide
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\item However, Hadley Wickham and Google developed style guides which are
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now widely accepted
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\begin{itemize}
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\item \url{https://google.github.io/styleguide/Rguide.html}
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\item \url{https://style.tidyverse.org/}
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\end{itemize}
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\item It is always a good idea to follow a style guide and not ``create''
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your own rules (if you deviate, be consistent!)
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\item A style guide helps with
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\begin{itemize}
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\item Keeping code clean which is easier to read and interpret
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\item Making it easier to catch and fix mistakes
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\item Making it easier for others to follow and adapt your code
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\item Preventing possible problems, e.\,g., avoiding dots in function
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names
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\end{itemize}
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\end{itemize}
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\nocite{Wickham_styleguide, Anderson2023}
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\end{frame}
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\begin{frame}[fragile, allowframebreaks]{File names}
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\begin{itemize}
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\item File names should be meaningful and end in .R
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\item Avoid using special characters in file names
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\item Stick with numbers, letters, \verb+-+, and \verb+_+
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\begin{lstlisting}[identifierstyle = \bfseries\color{iwmgray}]
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# Good
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fit_models.R
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utility_functions.R
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# Bad
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fit models.R
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foo.r
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stuff.r
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\end{lstlisting}
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\framebreak
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\item If files should be run in a particular order, prefix them with numbers
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\item If it seems likely you’ll have more than 10 files, left pad with zero
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\begin{lstlisting}[identifierstyle = \bfseries\color{iwmgray}]
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00_download.R
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01_explore.R
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...
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09_model.R
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10_visualize.R
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\end{lstlisting}
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\item If you later realize that you missed some steps, it’s tempting to use
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02a, 02b, etc.
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\item However, it is generally better to bite the bullet and rename all
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files
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile, allowframebreaks]{Object names}
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\begin{itemize}
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\item Variable and function names should use only lowercase letters,
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numbers, and \verb+_+
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\item Use underscores (\verb+_+) (so called snake case) to separate words
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within a name
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\begin{lstlisting}[identifierstyle = \bfseries\color{iwmgray}]
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# Good
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day_one
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day_1
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# Bad
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DayOne
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dayone
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\end{lstlisting}
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\framebreak
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\item Generally, variable names should be nouns and function names should be
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verbs
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\item Strive for names that are concise and meaningful
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\begin{lstlisting}[identifierstyle = \bfseries\color{iwmgray}]
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# Good
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day_one
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# Bad
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first_day_of_the_month
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djm1
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\end{lstlisting}
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\framebreak
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\item Avoid re-using names of common functions and variables
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\begin{lstlisting}
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# Bad
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T <- FALSE
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c <- 10
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mean <- function(x) sum(x)
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\end{lstlisting}
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile, allowframebreaks]{Spacing}
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\begin{itemize}
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\item Always put a space after a comma, never before
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\begin{lstlisting}
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# Good
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x[, 1]
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# Bad
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x[,1]
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x[ ,1]
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x[ , 1]
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\end{lstlisting}
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\framebreak
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\item Do not put spaces inside or outside parentheses for regular function
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calls
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\begin{lstlisting}
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# Good
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mean(x, na.rm = TRUE)
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# Bad
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mean (x, na.rm = TRUE)
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mean( x, na.rm = TRUE )
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\end{lstlisting}
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\framebreak
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\item Place a space before and after \texttt{()} when used with \texttt{if},
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\texttt{for}, or \texttt{while}
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\begin{lstlisting}
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# Good
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if (debug) {
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show(x)
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}
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# Bad
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if(debug){
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show(x)
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}
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\end{lstlisting}
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\framebreak
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\item Place a space after \texttt{()} used for function arguments
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\begin{lstlisting}
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# Good
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function(x) {}
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# Bad
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function (x) {}
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function(x){}
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\end{lstlisting}
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\framebreak
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\item Most infix operators (\verb+==+, \verb|+|, \verb+-+, \verb+<-+, etc.)
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should always be surrounded by spaces
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\begin{lstlisting}
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# Good
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height <- (feet * 12) + inches
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mean(x, na.rm = TRUE)
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# Bad
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height<-feet*12+inches
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mean(x, na.rm=TRUE)
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\end{lstlisting}
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\framebreak
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\item There are a few exceptions, which should never be surrounded by
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spaces: \verb+::+, \verb+:::+, \verb+$+, \verb+@+, \verb+[+, \verb+[[+,
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\verb+?+, \verb+^+, and \verb+:+
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{\small
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\begin{lstlisting}
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# Good
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sqrt(x^2 + y^2)
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df$z
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x <- 1:10
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package?stats
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?mean
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# Bad
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sqrt(x ^ 2 + y ^ 2)
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df $ z
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x <- 1 : 10
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package ? stats
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? mean
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\end{lstlisting}
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}
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\item Adding extra spaces is ok if it improves alignment of \verb+=+ or
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\verb+<-+
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\begin{lstlisting}
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# Good
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list(
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total = a + b + c,
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mean = (a + b + c) / n
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)
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# Also fine
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list(
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total = a + b + c,
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mean = (a + b + c) / n
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)
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\end{lstlisting}
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\end{itemize}
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\end{frame}
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% CITE:
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% https://style.tidyverse.org/index.html
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% R Programming for Reserach: https://geanders.github.io/RProgrammingForResearch/
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% Building reproducible analytical pipelines with R: https://raps-with-r.dev/
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\section{Script organisation}
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\begin{frame}[fragile]{Script header}
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\begin{itemize}
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\item It can be very helpful to have some general information right at the
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top when opening a script
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\begin{lstlisting}
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# 01_preprocessing.R
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#
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# Cleaning up toy data set (Methods Seminar SS2024)
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#
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# Input: rawdata/RDM_MS_SS2024_download_2024-06-07.csv
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# Output: processed/data_rdm-ms-ss2024_cleaned.csv
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# processed/data_rdm-ms-ss2024_cleaned.RData
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#
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# Created: 2024-06-03, NW
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\end{lstlisting}
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\item These metadata help you remember faster what you did
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\item Might not be necessary when using consistent version control (but does
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not hurt either)
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile]{Line length}
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{}
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\begin{center}
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{\Large\bf Keep lines to 80 characters or less!}
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\end{center}
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\begin{lstlisting}
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# Good
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my_df <- data.frame(n = 1:3,
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letter = c("a", "b", "c"),
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cap_letter = c("A", "B", "C"))
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# Bad
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my_df <- data.frame(n = 1:3, letter = c("a", "b", "c"), cap_letter = c("A", "B", "C"))
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\end{lstlisting}
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\begin{itemize}
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\item Ensures that your code is formatted in a way that you can see all of
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the code without scrolling horizontally
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\item To set your script pane to be limited to 80 characters, go to\\
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\verb+RStudio -> Preferences -> Code -> Display+\\
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and set ``Margin Column'' to 80
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile, allowframebreaks]{File organisation}
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\begin{itemize}
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\item Try to write scripts that are concerned with one (major) task
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\item If you can find a name, that captures the content, it is usually a
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good way to start
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\item Some (random) examples
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\begin{lstlisting}[identifierstyle = \bfseries\color{iwmgray}]
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download-data.R
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data-cleaning.R
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cluster_analysis_exp1.R
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visualization_logistic-model.R
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anova_h1.R
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\end{lstlisting}
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\framebreak
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\item Export data sets for new scripts (do not make yourself run all scripts
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up to script 5 each time, just because you need the data in a certain
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format)
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\begin{lstlisting}
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# Interoperable
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write.table(dat,
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file = "data_exp1_cleaned.csv",
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sep = ";",
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quote = FALSE,
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row.names = FALSE)
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# Preserve order of factor levels, date formats, etc.
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save(dat, file = "data_exp1_cleaned.RData")
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\end{lstlisting}
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\end{itemize}
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\end{frame}
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\begin{frame}[fragile, allowframebreaks]{Internal structure}
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\begin{itemize}
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\item Use commented lines with \texttt{-} or \texttt{=} to break your file
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up into chunks
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\item Load additional packages at the beginning of the script
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\begin{lstlisting}
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library(lme4)
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library(sjPlot)
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# Load data ---------------------------
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# Plot data ---------------------------
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\end{lstlisting}
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\framebreak
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\item If you load several packages, be aware that the order of loading
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matters!
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\item If you use only one or two functions from a package, get the function
|
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with \verb+::+ instead of loading the whole package
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\begin{lstlisting}
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library(lme4)
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...
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# Fit mixed-effects model to test Hypothesis 1
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lme1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
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summary(lme1)
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sjPlot::tab_model(lme1)
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\end{lstlisting}
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\framebreak
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\item Group related pieces of code together
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\item Separate blocks of code by empty spaces
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\begin{lstlisting}
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# Load data
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library(faraway)
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data(nepali)
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# Relabel sex variable
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nepali$sex <- factor(nepali$sex,
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levels = c(1, 2),
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labels = c("Male", "Female"))
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\end{lstlisting}
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\end{itemize}
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\end{frame}
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|
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\begin{frame}{How can I test if my code is reproducible?}
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% slido
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\centering
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||||
\includegraphics[width = 5cm]{../figures/QR Code for Methodenseminar SS 2024 - Session 5}
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|
||||
\url{https://app.sli.do/event/uEz8fJWkLBNm1sthQovXNH}
|
||||
\end{frame}
|
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\section{Code reviews}
|
||||
|
||||
\begin{frame}[<+->]{Use your peers}
|
||||
\begin{itemize}
|
||||
\item Do not overthink it!
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||||
\item Just give your data and code to a colleague and ask them to reproduce
|
||||
what you did (this sounds easy, but it is actually not!)
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\item This will give you tons of insights about your workflow
|
||||
\begin{itemize}
|
||||
\item Can this person (in general) understand what you did?
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||||
\item Is this person able to easily put your data on their machine and
|
||||
run the code right away?
|
||||
\item Anything this person would have done differently?
|
||||
\item Discuss why and which things you do differently
|
||||
\end{itemize}
|
||||
\item Reading other peoples's code is the best way to learn about how things
|
||||
can be done differently than you do them
|
||||
\item You can review code by printing it out and adding comments by hand\\
|
||||
(I highly recommend this!)
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\appendix
|
||||
%\begin{frame}[allowframebreaks]{References}
|
||||
\begin{frame}{References}
|
||||
%\renewcommand{\bibfont}{\small}
|
||||
\printbibliography
|
||||
\vfill
|
||||
\end{frame}
|
||||
|
||||
\end{document}
|
||||
|
||||
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figures/QR Code for Methodenseminar SS 2024 - Session 5.png
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@ -1,3 +1,11 @@
|
||||
@book{Anderson2023,
|
||||
title = {R programming for research},
|
||||
author = {Brooke Anderson and Rachel Severson and Nicholas Good},
|
||||
year = {2023},
|
||||
publisher = {Colorado State University, ERHS 535},
|
||||
url = {https://geanders.github.io/RProgrammingForResearch/}
|
||||
}
|
||||
|
||||
@article{Kathawalla2021,
|
||||
title = {Easing into open science: {A} guide for graduate students and their advisors},
|
||||
author = {Kathawalla, Ummul-Kiram and Silverstein, Priya and Syed, Moin},
|
||||
@ -61,6 +69,12 @@
|
||||
doi = {10.1016/j.intell.2012.01.004}
|
||||
}
|
||||
|
||||
@misc{Wickham_styleguide,
|
||||
author = {Hadley Wickham},
|
||||
title = {The tidyverse style guide},
|
||||
url = {https://style.tidyverse.org/}
|
||||
}
|
||||
|
||||
@misc{Wilbrandt2023,
|
||||
author = {Wilbrandt, Jeanne},
|
||||
title = {{Research Data Management Intro Series: Coffee Lectures \& Espresso Shots}},
|
||||
|
||||
Loading…
Reference in New Issue
Block a user