diff --git a/06_wrap_up/README.md b/06_wrap_up/README.md new file mode 100644 index 0000000..01774b7 --- /dev/null +++ b/06_wrap_up/README.md @@ -0,0 +1,23 @@ +# Last session: Wrap-up + +How to apply all we learned this semester to archiving our research data at the +IWM: + + +* Show how to fill in the input mask + +* Details on how to prepare data and folders + + Show slide set "How to know what to archive" + +* How to upload research data + +* How to create new version of research data + +* How to update meta data + +* Explain the "Status" mechanism + +* Show that only one person per data set has access to the meta data entry + + diff --git a/06_wrap_up/howto_what-to-archive.tex b/06_wrap_up/howto_what-to-archive.tex new file mode 100644 index 0000000..25c158f --- /dev/null +++ b/06_wrap_up/howto_what-to-archive.tex @@ -0,0 +1,408 @@ +\documentclass[aspectratio=169]{beamer} + +\usepackage{tikz} +\usetikzlibrary{fit} + +\usepackage{listings} +\usepackage[utf8,latin1]{inputenc} +\usepackage{multirow} +\usepackage{color, colortbl} +\usepackage{fontawesome5} % get icons + +\makeatletter \def\newblock{\beamer@newblock} \makeatother + +\beamertemplatenavigationsymbolsempty +\setbeamertemplate{itemize items}[circle] +\setbeamertemplate{section in toc}[circle] +\mode{\setbeamercolor{math text displayed}{fg=iwmgrau}} +\setbeamercolor{block body}{bg=iwmorange!50!white} +\setbeamercolor{block title}{fg=white, bg=iwmorange} + +\definecolor{iwmorange}{RGB}{255,105,0} +\definecolor{iwmgray}{RGB}{67,79,79} +\definecolor{iwmblue}{RGB}{60,180,220} +\definecolor{iwmpurple}{RGB}{120,0,75} + +\definecolor{iwmorange}{RGB}{255,105,0} +\definecolor{iwmgrau}{RGB}{67,79,79} +\setbeamercolor{title}{fg=iwmorange} +\setbeamercolor{frametitle}{fg=iwmorange} +\setbeamercolor{structure}{fg=iwmorange} +\setbeamercolor{normal text}{fg=iwmgrau} +\setbeamercolor{author}{fg=iwmgrau} +\setbeamercolor{date}{fg=iwmgrau} + +\lstset{language=bash,% + literate={Ü}{{\"U}}1 + {ü}{{\"u}}1, + backgroundcolor=\color{iwmgrau!15!white}, + basicstyle=\ttfamily\color{iwmgrau}, + frame=none, + basicstyle=\ttfamily\color{iwmgrau}, + commentstyle=\slshape\color{iwmgrau}, + keywordstyle=\bfseries\color{iwmgrau}, + identifierstyle=\color{iwmgrau}, + stringstyle=\color{iwmgrau}, + numbers=none,%left,numberstyle=\tiny, + basewidth={.5em, .4em}, + showstringspaces=false, + emphstyle=\color{red!50!white}} + +\pgfmathdeclarefunction{gauss}{2}{% + \pgfmathparse{1/(#2*sqrt(2*pi))*exp(-((x-#1)^2)/(2*#2^2))}% +} + +\AtBeginSection[]{ + \frame{ + \tableofcontents[sectionstyle=show/hide, subsectionstyle=show/show/hide]}} + +% \setbeamertemplate{headline}{ +% \begin{beamercolorbox}{section in head} +% \vskip5pt\insertsectionnavigationhorizontal{\paperwidth}{}{}\vskip2pt +% \end{beamercolorbox} +% } + +\setbeamertemplate{footline}{\vskip-2pt\hfill\insertframenumber$\;$\vskip2pt} + + +\title{How to know what to archive} +\author{Nora Wickelmaier} +\date{\today} + +\begin{document} + +\begin{frame}{} +\thispagestyle{empty} +\titlepage +\end{frame} + +\begin{frame}{The basics} + Data + \begin{itemize} + \item Keep your raw data in a separate folder + \item If your raw data \emph{do not contain any personal data} submit them + with your analysis-ready data files + \item Submit the analysis script that got your raw data to + ``analysis-ready`` (or at least a description of the process)\pause\hfill + {\bf\color{iwmpurple} Check out our Research Data Policy!} + \end{itemize} + \pause + Material + \begin{itemize} + \item Submit all materials that have been used to create these data + \begin{itemize} + \item Questionnaires + \item Program code for experiments + \item Stimuli presented, e.\,g., pictures or similar + \item \dots + \end{itemize} + \end{itemize} + \pause + Documentation + \begin{itemize} + \item Add a description of your data and experiment + \item In its simplest form this can just be a README file, ideally as text + or PDF file + \end{itemize} +\end{frame} + +\begin{frame}[fragile]{Previous folder structure on \texttt{Y:/}} + \begin{columns} + \begin{column}{.4\textwidth} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+data+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+ethik+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+pub+}; + \node (n5) at (4, -2.8) {\faIcon{folder} \verb+scans+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (n5.west); + \end{tikzpicture} + \end{column} + \begin{column}{.6\textwidth} + \begin{itemize}[<+->] + \item Very basic (and good) folder structure for a research project + \item Submitting the approval document of our \emph{local} ethics + committee is now optional, since the connection will be possible via + your meta data\\ + % $\to$ If the project was evaluated by an external ethics committee it + % might still be a good idea to submit the approval document + \item Data and material are the most important folders to help other + people make sense of your data + \end{itemize} + \end{column} + \end{columns} + \vfill +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \vspace{.2cm} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + \end{tikzpicture} + \pause + \vfill + Separate your code from your data folder and add your preregistration for the + project +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + % second level + \node[text width = 5cm] (o1) at (10, 0) {\faIcon[regular]{file} \verb+01_preprocessing.R+}; + \node[text width = 5cm] (o2) at (10, -0.7) {\faIcon[regular]{file} \verb+02_descriptives.R+}; + \node[text width = 5cm] (o3) at (10, -1.4) {\faIcon[regular]{file} \verb+03_modeling.R+}; + \node[text width = 5cm] (o4) at (10, -2.1) {\faIcon[regular]{file} \verb+04_plots.R+}; + \path (n1.east) -- (o1.west); + \path (n1.east) -- (o2.west); + \path (n1.east) -- (o3.west); + \path (n1.east) -- (o4.west); + \end{tikzpicture} + \vfill + Separate your code from your data folder and add your preregistration for the + project +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + % second level + \node[text width = 6cm] (o1) at (10.5, -0.7) {\faIcon{folder} \verb+01_raw-data+}; + \node[text width = 6cm] (o2) at (10.5, -1.4) {\faIcon{folder} \verb+02_processed-data+}; + \node[text width = 6cm] (o3) at (10.5, -2.1) {\faIcon[regular]{file} + \verb+codebook_processed-data.pdf+}; + \path (n2.east) -- (o1.west); + \path (n2.east) -- (o2.west); + \path (n2.east) -- (o3.west); + \end{tikzpicture} + \vfill + Separate your code from your data folder and add your preregistration for the + project +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + % second level + \node[text width = 5cm] (o1) at (10, -1.4) {\faIcon{folder} \verb+stimuli+}; + \node[text width = 5cm] (o2) at (10, -2.1) {\faIcon[regular]{file} \verb+survey01.pdf+}; + \node[text width = 5cm] (o3) at (10, -2.8) {\faIcon[regular]{file} \verb+survey02.pdf+}; + \path (n3.east) -- (o1.west); + \path (n3.east) -- (o2.west); + \path (n3.east) -- (o3.west); + \end{tikzpicture} + \vfill +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \vspace{.4cm} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + % second level + \node[text width = 6cm] (o1) at (10.5, -2.1) {\faIcon[regular]{file} \verb+2024-06-11_prereg_study.pdf+}; + \path (n4.east) -- (o1.west); + \end{tikzpicture} + \pause + \vfill + A preregistration usually contains all important information like what + variables have been collected, what were the hypotheses, etc. +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \begin{columns} + \begin{column}{.45\textwidth} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -2.8) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (file.west); + \end{tikzpicture} + \end{column} + \begin{column}{.55\textwidth} + \vspace{-3cm} + \begin{itemize} + \item Add any additional folders that you need + \end{itemize} + \end{column} + \end{columns} +\end{frame} + + +\begin{frame}[fragile]{Some additional suggestions} + \vspace{1cm} + \begin{columns} + \begin{column}{.45\textwidth} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \bf background}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+code+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+data+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+material+}; + \node (n5) at (4, -2.8) {\faIcon{folder} \verb+preregistration+}; + \node (file) at (4, -3.5) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (n5.west); + \path (top.east) -- (file.west); + \end{tikzpicture} + \end{column} + \begin{column}{.55\textwidth} + \vspace{-2.5cm} + \begin{itemize} + \item Add any additional folders that you need + \item Maybe a folder \verb+background+ with a PhD expos{\'e} or a grant + application (or both) + \end{itemize} + \end{column} + \end{columns} + \vfill +\end{frame} + +\begin{frame}[fragile]{Some additional suggestions} + \vspace{.5cm} + \begin{columns} + \begin{column}{.45\textwidth} + \begin{tikzpicture}[ + every node/.style = {text width = 3.6cm, align = left}, + every path/.style = {thick, draw} + ] + \node[text width = 2cm] (top) at (0, 0) {\faIcon{folder} \verb+study+}; + % first level + \node (n1) at (4, 0) {\faIcon{folder} \verb+code+}; + \node (n2) at (4, -0.7) {\faIcon{folder} \verb+data+}; + \node (n3) at (4, -1.4) {\faIcon{folder} \verb+material+}; + \node (n4) at (4, -2.1) {\faIcon{folder} \verb+preregistration+}; + \node (n5) at (4, -2.8) {\faIcon{folder} \bf software}; + \node (file) at (4, -3.5) {\faIcon[regular]{file} \verb+README.md+}; + \path (top.east) -- (n1.west); + \path (top.east) -- (n2.west); + \path (top.east) -- (n3.west); + \path (top.east) -- (n4.west); + \path (top.east) -- (n5.west); + \path (top.east) -- (file.west); + \end{tikzpicture} + \end{column} + \begin{column}{.55\textwidth} + \begin{itemize} + \item Add any additional folders that you need + \item Maybe a folder \verb+background+ with a PhD expos{\'e} or a grant + application (or both) + \item Or a folder \verb+software+ with Python or Matlab code that you + wrote for your experiment + \item \dots + \end{itemize} + \vfill + \end{column} + \end{columns} +\end{frame} + + +\begin{frame}{} + {} + \begin{center} + {\Huge\color{iwmblue} Don't overthink it and use common sense.\\ + \vspace{1cm}\pause + Then add everything that you think a colleague needs to understand what you + did.} + \end{center} + +\end{frame} + +\end{document} + diff --git a/README.md b/README.md index 5a1a50f..db1eb67 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ | 2024-06-10 | Data organisation | | 2024-06-24 | Data sharing | | 2024-07-08 | Clean coding | -| 2024-07-22 | Version control | +| 2024-07-22 | Archiving data at the IWM | # Literature