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<!doctype html>
<html lang="en">
<head>
<!-- Required meta tags -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=Yes">
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<title>Open Science: Fun & Easy!</title>
</head>
<body>
<nav class="navbar navbar-expand-lg navbar-light bg-light">
<a class="navbar-brand" href="https://github.com/vanatteveldt/compendium-checklist" target="_blank">
<h1>Compendium Checklist to Make Open Science Fun & Easy!</h1>
<i>Wouter van Atteveldt, Anne Kroon, Felicia Loecherbach, Mickey Steijaert, Joanna Strychach,
Damian Trilling, Mariken A.C.G. van der Velden & Kasper Welbers </i> </a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="true" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
</nav>
<div class="container-fluid" style="padding-bottom: 1em; padding-top: 1em; padding-left: 5em; padding-right: 5em">
<ul class="nav navbar-dark bg-dark nav-pills" style="padding-bottom: 0" role="tablist" id="topictabs">
<li class="nav-item pill">
<a class="nav-link active" id="pillphase1" data-toggle="tab" role="tab"
href="#phase1" aria-controls="phase1" aria-selected="True">
1. Getting Started
</a>
</li>
<li class="nav-item pill">
<a class="nav-link " id="pillphase2" data-toggle="tab" role="tab"
href="#phase2" aria-controls="phase2" aria-selected="False">
2. Version Control for Your Program/Language
</a>
</li>
<li class="nav-item pill">
<a class="nav-link " id="pillphase3" data-toggle="tab" role="tab"
href="#phase3" aria-controls="phase3" aria-selected="False">
3. Structure of Your Project Folders
</a>
</li>
<li class="nav-item pill">
<a class="nav-link " id="pillphase4" data-toggle="tab" role="tab"
href="#phase4" aria-controls="phase4" aria-selected="False">
4. Checks Before Submitting Your Manuscript
</a>
</li>
</ul>
<div class="tab-content" id="topictabscontent">
<div class="tab-pane fade show active" id="phase1"
role="tabpanel" aria-labelledby="phase1-tab" style="margin-left: 1em; margin-right: -1em;padding-right: 2em">
<h3>Welcome to our Compendium Checklist!</h3> <hr />
<p> This website created by the <a href = "http://ccs.amsterdam/" target="_blank">Computational Communication Science Amsterdam</a>
is designed to walk you through the different steps of creating an <em>Open Science Compendium</em> for your own research project.
The whole process is divided into four phases (on the top) and for each phase you can answer questions that are either aimed at reminding you
of things that need to be done or give you additional information on what to install/how to set things up if you are not yet familiar with it.
On the right side you will see additional information and links.
The first couple of questions are checking whether the computer you are working on for this research project has all necessary
applications to work with the <a href = "https://github.com/ccs-amsterdam/compendium" target="_blank"> Standardized Research Compendium</a>.
</br></br>
<ins>Feel free to <a href="#" onclick="skiptotab(3)">skip the first two phases</a>, if you have worked with our Standardized Research Compendium before,
or feel that you do not need any information or help for those parts. You can always go back to earlier phases.</ins>
<div class="row question " id="Q1_1">
<div class="col-md-6 qquestion" style="padding-right: 2em">
<p class="lead"> <b>Is it the first time you are working with Version Control?</b> </p>
<p> Version control is a system that records changes to a file or set of files over time so that you can recall or restore specific versions later. Working with a version control system increases the transparancy of your project. </p>
</div>
<div class="col-md-2 qcheck">
<div class="btn-group btn-group-toggle" data-toggle="buttons">
<label class="btn btn-yes yes" onclick="toggle('Q1_1', true)">
<input type="radio" name="options" id="#Q1_1_yes" onclick="event.stopPropagation()">Yes
</label>
<label class="btn btn-no no" onclick="toggle('Q1_1', false)">
<input type="radio" name="options" id="#Q1_1_no" onclick="event.stopPropagation()">No
</label>
</div>
</div>
<div class="col-md-4 qadvice">
<div class="collapse" id="Q1_1_no_advice">
<p >I know version control and have worked with it before. </br> </br> If you want to (re)visit or look up some principles of working with version control, you can find a comprehensive documentation <a href="https://git-scm.com/book/en/v2/" target="_blank"> here</a>.</p>
</div>
<div class="collapse" id="Q1_1_yes_advice">
<p>Ever produced a text document, script or datafile with a title looking like this: <em>"FinalVersion2.0_REVISITED18may_FL"</em>?</br> Click on more information to learn how to organize your scripts in a reproducible, open, and transparent manner, and an additional advantage, you wil no longer produce files with such titles.</p>
<!-- Button to Open the Modal -->
<div class="col text-center">
<button type="button" class="btn btn-primary" data-toggle="modal" data-target="#myModal" >
<b> More Information</b>
</button>
</div>
<!-- The Modal -->
<div class="modal fade" id="myModal">
<div class="modal-dialog modal-dialog-centered">
<div class="modal-content">
<!-- Modal Header -->
<div class="modal-header">
<h4 class="modal-title" id="Q1_1_info_box_header">Version control</h4>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<!-- Modal body -->
<div class="modal-body">
<p> When working on vast, collaborative scientific projects, keeping track of different versions of your work can be a burden. Still, it is important to store older versions - not only because you might want to revert changes later on in the process, but also because you want to get insight into what changes your coworkers made to your precious file. <br/> <br/> Luckily, there now exist digital version control systems, that make version control easy and understandable. Such version control systems save not only new files that you save to the system, but also the changes between the old and new version. This way, you can easily keep track of changes and revert to old versions (or even combine different "branches" of a file) as you please. <br/><br/> Right now, the most popular software amongst scientists for doing this is Git, a prrogram that manages "repositories" (the "folder" with your project), which stores files and each file's revision history. <a href="https://github.com/" target="_blank"> Github.com </a> is an cloud web server which offers the opportunity to store your repository remotely, to easily collabore on projects with colleagues. A comprehensive documentation on getting started with Git can be found <a href="https://git-scm.com/book/en/v2/" target="_blank"> here</a>. </p>
</div>
<!-- Modal footer -->
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row question " id="Q1_2">
<div class="col-md-6 qquestion" style="padding-right: 2em">
<p class="lead"> <b>Is it the first time you are working with Git, Python, and <em>doit</em> on your current computer?</b> </p>
<p> To work with the Standardized Research Compendium, you need to have Python Version XX, the package <em>doit</em>, and Git installed on your current computer. </p>
</div>
<div class="col-md-2 qcheck">
<div class="btn-group btn-group-toggle" data-toggle="buttons">
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<label class="btn btn-no no" onclick="toggle('Q1_2', false)">
<input type="radio" name="options" id="#Q1_2_no" onclick="event.stopPropagation()">No
</label>
</div>
</div>
<div class="col-md-4 qadvice">
<div class="collapse" id="Q1_2_no_advice">
<p >I have all of this installed. </br> </br> If you want to look into the advantages of the combination of Git, Python and <em>doit</em>, have a look at <a href = "https://github.com/ccs-amsterdam/compendium" target="_blank"> our GitHub page</a>. </p>
</div>
<div class="collapse" id="Q1_2_yes_advice">
<p>I need help with it</p>
<!-- Button to Open the Modal -->
<div class="col text-center">
<button type="button" class="btn btn-primary" data-toggle="modal" data-target="#myModal" >
<b> More Information</b>
</button>
</div>
<!-- The Modal -->
<div class="modal fade" id="myModal">
<div class="modal-dialog modal-dialog-centered">
<div class="modal-content">
<!-- Modal Header -->
<div class="modal-header">
<h4 class="modal-title" id="Q1_2_info_box_header">Working from a Terminal</h4>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<!-- Modal body -->
<div class="modal-body">
<p> Add info for Windows, Mac and Linux. </p>
</div>
<!-- Modal footer -->
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row question collapse" id="Q1_3">
<div class="col-md-6 qquestion" style="margin-left: 2em; margin-right: -2em;padding-right: 2em">
<p class="lead"> <b>Is this the first time you are working with Git on this computer?</b> </p>
<p> <a href="https://en.wikipedia.org/wiki/Git" target="_blank"> Git</a> is a distributed version-control system for tracking changes in source code during software development.</p>
</div>
<div class="col-md-2 qcheck">
<div class="btn-group btn-group-toggle" data-toggle="buttons">
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<p >I have Git installed on this computer. </br> </br> You can find a comprehensive documentation of working with Git <a href="https://git-scm.com/book/en/v2/" target="_blank"> here</a>.</p>
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<p>I need help with it.</p>
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<p> Installing the digital version control system Git is easy - but works differently depending on your operating system.
Visit this webpage to find the specific installation manual for your operating system:
https://gist.github.com/derhuerst/1b15ff4652a867391f03 </p>
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<p class="lead"> <b>Is this the first time you are working with Python version x on your current computer?</b> </p>
<p> <a href="https://en.wikipedia.org/wiki/History_of_Python" target="_blank"> Python has developed over time</a>, using different version can cause conflicts with the proposed workflow of the Standardized Research Compendium.</p>
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<p >I have this Python version installed. </br> </br> You can find elaborate documentation on working with Python <a href="https://wiki.python.org/moin/" target="_blank">here</a>.</p>
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<p>I have not yet installed this Python version. </p>
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<p> Python is a programming language that is used by professionals from a wide variety of fields to write software. In Python, many packages (small programs) are written that offer you a specific type of functionality, like the 'doit'-package that we use in the compendium.
Visit this webpage to find the specific installation manual for your operating system:
https://wiki.python.org/moin/BeginnersGuide/Download </p>
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<p class="lead"> <b>Is it the first time you will be working with the Python package <a href="https://pydoit.org/contents.html" target="_blank"> <em>doit</em></a> on the current computer?</b> </p>
<p> <em>doit</em> is a modern open-source build-tool written in python designed to be simple to use and flexible to deal with complex work-flows.</p>
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<p >I have run <code>pip install doit</code> and thereby have installed <em>doit</em> on my computer. </br> </br> You can find more information on <em>doit</em> <a href="https://pydoit.org/" target="_blank">here</a>.</p>
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<p>I need help with it.</p>
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<p> Doit is a powerful automation tool Python package. Simply put, it is a package that enables you to define simple tasks for a program to perform (like building and maintaining a research compendium!). Visit this page for more information about doit: https://pydoit.org/index.html
To install doit, simply type "pip3 install doit" (Windows) or "sudo pip3 install doit" (Linux / Mac) in the terminal.
Note: 'pip' is a package installer for Python, which mostly comes pre-installed with your Python version. If, for whatever reason, you have to (re-)install pip, visit this website for an installation guide for different systems: https://pip.pypa.io/en/stable/ </p>
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<p class="lead"> <b>Is it the first time you are creating a version control repository? Or is a version control repository for this project non-existing?</b> </p>
<p> Create a version control repository on <a href="https://github.com/" target="_blank">GitHub</a> or a similar provider, such as <a href="https://bitbucket.org/product" target="_blank"> Bitbucket</a>. Doing this from the start and using a version control repositoty to collaborate internally is a good strategy to ensure all needed data and scripts are always accessable. <a href="https://github.com/" target="_blank">GitHub</a> and other providers allow for private repositories for academic use. </p>
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<p >I have created a version control repo.</br> </br> You can find a comprehensive documentation of working with a Git repo <a href="https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-Repository" target="_blank"> here</a>.</p>
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<p>I need help with it.</p>
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<h4 class="modal-title" id="Q1_6_info_box_header">The compendium structure</h4>
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<p> To make your project easily understandable and interpetable for others, we advise you to use our standardized research compendium for structuring your project. To do so, we explain you how to copy the blueprint for this structure in the next step.
If you still feel like creating your own folder structure, you can visit this webpage to learn how to create a Github repository: https://help.github.com/en/github/getting-started-with-github/create-a-repo </p>
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<p class="lead"> <b>Is it the first time you are going to fork, copy or clone the Version Control Structure proposed by the Standardized Research Compendium?</b> </p>
<p> You can find the Version Control Structure proposed by the Standardized Research Compendium on the <a href="https://github.com/ccs-amsterdam/compendium" target="_blank"> authors’ GitHub page</a>.</p>
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<p >I have forked, copied or cloned the Version Control Structure from the authors’ Github page.. </br> </br> Here you can find a comprehensive documentation of <a href="https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project" target="_blank"> forking</a>,<a href="https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-Repository" target="_blank"> copying</a>, or <a href="https://git-scm.com/docs/git-clone" target="_blank"> cloning</a>.</p>
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<p>I need help with it.</p>
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<p> By 'forking' a repository on Github, you simply make your own copy of the repository which you can subsequently edit as you see fit. We advise you to fork the basic folder structure template from Github, to ensure that your project adheres to the standardized folder structure. You can find the template here: https://github.com/ccs-amsterdam/compendium
To fork the template, go to the template page and click 'Fork' button on the top right corner of the screen. </p>
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<p class="lead"> <b>Do you need help or would you like more information about running <code>doit install</code> in the command line to set up the necessary Python and/or R environment for you research project?</b> </p>
<p> For the workflow, <code> doit install </code> is essential for the workflow of the Standardized Research Compendium. This will set up the necessary Python and/or R environment.</p>
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<p >I have run <code>doit install</code> or know how to do it.</br> </br> You can find more information on installing <em>doit</em> <a href="https://pydoit.org/install.html" target="_blank">here</a>.</p>
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<p>I need help with it.</p>
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<p> To get your repository up and running, you have to access the doit package to install all neccessary Python and/or R components to have your project all set up.
This is done simply by opening your terminal, nagivating to your repository and running "doit install". </p>
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<p class="lead"> <b>Have you considered pre-registering your study?</b> </p>
<p> Preregistration is the practice of documenting your research plan at the beginning of your study and storing that plan in a read-only public repository. For an overview of registry services, see <a href="https://osf.io/registries" target="_blank"> OSF Registries</a>.</p>
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<p >Pre-registration is not applicable for my study (anymore). </br> </br> For research that uses existing datasets, there is an increased risk of analysts being biased by preliminary trends in the dataset. <a href="https://osf.io/x4gzt/" target="_blank"> This page</a> provides a framework for preregistering studies that use existing data. </p>
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<div class="collapse" id="Q1_9_yes_advice">
<p>I plan to preregister my study. </br> </br> <a href="https://www.nature.com/articles/s41562-019-0772-6" target="_blank">This article</a>, published in <em>Nature</em>, entitled <i>A Consensus-Based Transparency Checklist</i> aims to improve and document the transparency of research reports in social and behavioural research. Their accompanying <a href="http://www.shinyapps.org/apps/TransparencyChecklist/" target="_blank">online application</a> allows users to answer a series of questions and generates a report that they can submit with their manuscript or post to a public repository.</p>
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<h3>Set-Up Your Project's Version Control!</h3> <hr />
<p>These questions allow you to set up the version control for the program and/or language you are working with when conducting your research.
If you think you do not need any explanations regarding this part, <a href="#" onclick="skiptotab(3)">you can just skip it</a>. </p>
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<p class="lead"> <b>Does your project use Python?</b> </p>
<p> <a href="https://www.python.org/" target="_blank">Python</a> is an interpreted, high-level, general-purpose programming language.</p>
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<p class="lead"> <b>Do you need help with <a href="https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/" target="_blank">activating the environment</a> for version control of the package?</b> </p>
<p> Explain <code>dodo.py</code></p>
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<p >I need help with it.</p>
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<p>I have activated it.</p>
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<p class="lead"> <b>Does your project use R?</b> </p>
<p> <a href="https://www.r-project.org/about.html" target="_blank">R</a> is a programming language for statistical computing and graphics. If you are a beginning user of R, please visit the <a href="https://github.com/ccs-amsterdam/r-course-material" target="_blank">CCS GitHub page</a> for tutorials.</p>
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<p class="lead"> <b>Is it the first you will be working with the <em>packrat</em> package?</b> </p>
<p> <a href="https://rstudio.github.io/packrat/" target="_blank"><em>packrat</em></a> is a dependency management system for R packages.</p>
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<p >I have installed <em>packrat</em> or worked with it before. </br> </br> You can find information about the <em>packrat</em> package <a href="https://cran.r-project.org/web/packages/packrat/index.html" target="_blank">here</a>, or you can visit the short online tutorial <a href="https://rstudio.github.io/packrat/" target="_blank">here</a> to revisit some of the <em>packrat</em> principles.</p>
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<p>I need help with it.</p>
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<p class="lead"> <b>Does your project use another – not open source – analysis language?</b> </p>
<p> If you used SPSS/Stata/SAS/MatLab/Atlas TI or anything else.</p>
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<p ></p>
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<p>Add what to do to make the compendium reproducible</p>
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<p class="lead"> <b>Do you install any extensions when cleaning, processing and/or analyzing the data in your research project?</b> </p>
<p> Proprietary data refers to any set of statistics, information, or documentation which is controlled solely by you or a third party. The data is typically protected by copyright law, trade secret laws, and even by patent agreement, in some cases.</p>
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<p >I have not installed any extensions.</p>
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<p>I have installed extensions.</p>
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