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<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head> <meta charset="utf-8"> <meta name="generator" content="quarto-1.6.37"> <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes"> <title>readme</title> <style> code{white-space: pre-wrap;} span.smallcaps{font-variant: small-caps;} div.columns{display: flex; gap: min(4vw, 1.5em);} div.column{flex: auto; overflow-x: auto;} div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} ul.task-list{list-style: none;} ul.task-list li input[type="checkbox"] { width: 0.8em; margin: 0 0.8em 0.2em -1em; /* quarto-specific, see quarto-dev/quarto-cli#4556 */ vertical-align: middle; } </style> <script src="README_files/libs/clipboard/clipboard.min.js"></script> <script src="README_files/libs/quarto-html/quarto.js"></script> <script src="README_files/libs/quarto-html/popper.min.js"></script> <script src="README_files/libs/quarto-html/tippy.umd.min.js"></script> <script src="README_files/libs/quarto-html/anchor.min.js"></script> <link href="README_files/libs/quarto-html/tippy.css" rel="stylesheet"> <link href="README_files/libs/quarto-html/quarto-syntax-highlighting-29e2c20b02301cfff04dc8050bf30c7e.css" rel="stylesheet" id="quarto-text-highlighting-styles"> <script src="README_files/libs/bootstrap/bootstrap.min.js"></script> <link href="README_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet"> <link href="README_files/libs/bootstrap/bootstrap-7e3a3fbe7cdabbbce03495fb14b8c7aa.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light"> </head> <body class="fullcontent"> <div id="quarto-content" class="page-columns page-rows-contents page-layout-article"> <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"></header> <!-- README.md is generated from README.Rmd. Please edit that file --> <section id="skps" class="level1"> <h1>SKPs</h1> <div class="quarto-figure quarto-figure-center"> <figure class="figure"> <p><a href="https://mybinder.org/v2/gh///master?urlpath=rstudio"><img src="https://mybinder.org/badge_logo.svg" class="img-fluid figure-img" alt="Binder"></a></p> <figcaption>Binder</figcaption> </figure> </div> <p>The current system of scientific knowledge dissemination, primarily relying on PDF-based journal articles, presents significant challenges in terms of reproducibility, interoperability, and reusability. We propose a novel approach: Scientific Knowledge Packages (SKPs). SKPs are self-contained, modular units of scientific knowledge, encompassing data, code, metadata, and results in a standardized, human- and machine-readable formats. This proposal outlines the structure, metadata specifications, and potential benefits of SKPs, aiming to enhance scientific communication and collaboration.</p> <p>This repository contains the data and code for our paper:</p> <blockquote class="blockquote"> <p>Authors, (2025). <em>A Proposal for Scientific Knowledge Packages (SKPs): A Modular and Reproducible Alternative to Traditional Scientific Publications</em>. Name of journal TBA <a href="https://doi.org/xxx/xxx" class="uri">https://doi.org/xxx/xxx</a></p> </blockquote> <p>Our pre-print is online here:</p> <blockquote class="blockquote"> <p>Authors, (2025). <em>A Proposal for Scientific Knowledge Packages (SKPs): A Modular and Reproducible Alternative to Traditional Scientific Publications</em>. TBA, Accessed 11 Apr 2025. Online at <a href="https://doi.org/xxx/xxx" class="uri">https://doi.org/xxx/xxx</a></p> </blockquote> <section id="how-to-cite" class="level3"> <h3 class="anchored" data-anchor-id="how-to-cite">How to cite</h3> <p>Please cite this compendium as:</p> <blockquote class="blockquote"> <p>Authors, (2025). <em>Compendium of R code and data for A Proposal for Scientific Knowledge Packages (SKPs): A Modular and Reproducible Alternative to Traditional Scientific Publications</em>. Accessed 11 Apr 2025. Online at <a href="https://doi.org/xxx/xxx" class="uri">https://doi.org/xxx/xxx</a></p> </blockquote> </section> <section id="contents" class="level2"> <h2 class="anchored" data-anchor-id="contents">Contents</h2> <p>The <strong>analysis</strong> directory contains:</p> <ul> <li><a href="./analysis/paper">:file_folder: paper</a>: Quarto source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered version, <code>paper.docx</code>, suitable for reading (the code is replaced by figures and tables in this file)</li> <li><a href="./analysis/data">:file_folder: data</a>: Data used in the analysis.</li> <li><a href="./analysis/figures">:file_folder: figures</a>: Plots and other illustrations</li> <li><a href="./analysis/supplementary-materials">:file_folder: supplementary-materials</a>: Supplementary materials including notes and other documents prepared and collected during the analysis.</li> </ul> </section> <section id="how-to-run-in-your-browser-or-download-and-run-locally" class="level2"> <h2 class="anchored" data-anchor-id="how-to-run-in-your-browser-or-download-and-run-locally">How to run in your browser or download and run locally</h2> <p>This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the <a href="https://cloud.r-project.org/">R software</a> itself and optionally <a href="https://rstudio.com/products/rstudio/download/">RStudio Desktop</a>.</p> <p>You can download the compendium as a zip from from this URL: <a href="./archive/master.zip">master.zip</a>. After unzipping: - open the <code>.Rproj</code> file in RStudio - run <code>devtools::install()</code> to ensure you have the packages this analysis depends on (also listed in the <a href="./DESCRIPTION">DESCRIPTION</a> file). - finally, open <code>analysis/paper/paper.Rmd</code> and knit to produce the <code>paper.docx</code>, or run <code>rmarkdown::render("analysis/paper/paper.qmd")</code> in the R console</p> <section id="licenses" class="level3"> <h3 class="anchored" data-anchor-id="licenses">Licenses</h3> <p><strong>Text and figures :</strong> <a href="http://creativecommons.org/licenses/by/4.0/">CC-BY-4.0</a></p> <p><strong>Code :</strong> See the <a href="DESCRIPTION">DESCRIPTION</a> file</p> <p><strong>Data :</strong> <a href="http://creativecommons.org/publicdomain/zero/1.0/">CC-0</a> attribution requested in reuse</p> </section> <section id="contributions" class="level3"> <h3 class="anchored" data-anchor-id="contributions">Contributions</h3> <p>We welcome contributions from everyone. Before you get started, please see our <a href="CONTRIBUTING.md">contributor guidelines</a>. Please note that this project is released with a <a href="CONDUCT.md">Contributor Code of Conduct</a>. 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