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<!DOCTYPE html>
<html lang="en"><head>
<script src="renv_files/libs/clipboard/clipboard.min.js"></script>
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<meta name="author" content="RStudio/Posit Solutions Engineering (Lisa Anders)">
<title>Reproduceable Workflows</title>
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<section id="title-slide" class="center">
<h1 class="title">Reproduceable Workflows</h1>
<p class="author">RStudio/Posit Solutions Engineering (Lisa Anders)</p>
<p class="institute">RStudio, PBC</p>
</section>
<section>
<section id="outline" class="title-slide slide level1 smaller center">
<h1>Outline</h1>
<ul>
<li>The data science workflow</li>
<li>New tools and tricks: Development, Sharing, and Production</li>
<li>Environment Management Strategies: Using renv and public package manager</li>
<li>Case Study</li>
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<aside class="notes">
<p>Press the S key (or use the Navigation Menu) to show the presentation speaker view (multiplex).</p>
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<!-- ## What is R? {.smaller} -->
<!-- {width="250"} -->
<!-- R is a **free and open-source** software environment for **statistical computing and graphics**. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. -->
</section>
<section id="data-science-workflow" class="slide level2">
<h2>Data Science Workflow</h2>
<center>
<p><img data-src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/data_cowboy.png" style="width:70.0%"></p>
<p><strong>Develop</strong> -> <strong>Share</strong> -> <strong>Productionize</strong></p>
<div class="citation" style="font-size: 16px">
<p>“Illustration from Hadley Wickham’s talk”The Joy of Functional Programming (for Data Science).” by <a href="https://github.com/allisonhorst/stats-illustrations">Allison Horst</a></p>
</div>
</center>
<aside class="notes">
<p>Development: - Writing effective code - Connecting to data sources and systems</p>
<p>Sharing: - Sharing outputs and securing access - Delivering actionable insights</p>
<p>Production: - Code reproduceability - Managing packages and reproducing environments - Collaborating with team members - Implementing operational workflows and scaling</p>
<p>Story segue. Manufacturing monitors project. Transferring code, hosting the output, challenges with numbers being different from other reports.</p>
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<section id="new-tools-and-tricks-development" class="slide level2 smaller">
<h2>New tools and tricks: Development</h2>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://www.tidymodels.org/images/tidymodels.png" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>tidymodels</strong> - The tidymodels framework is a collection of packages for modeling and machine learning using tidyverse principles.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
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<p><img data-src="https://rstudio.github.io/vetiver-r/logo.png" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>vetiver</strong> - Vetiver provides fluent tooling to version, deploy, and monitor a trained model.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://pins.rstudio.com/logo.png" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>pins</strong> - The pins package publishes data, models, and other R objects, making it easy to share them across projects and with your colleagues.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://d33wubrfki0l68.cloudfront.net/9f64516ebe93a8e5c91ea7409cbf422f8fec00e9/d75bd/logo.svg" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>plumber APIs</strong> - Plumber allows you to create a web API by merely decorating your existing R source code with roxygen2-like comments.</p>
</div>
</div>
</div>
<center>
<div class="citation" style="font-size: 16px">
<p>tidymodels <a href="https://www.tidymodels.org/" class="uri">https://www.tidymodels.org/</a>, vetiver <a href="https://vetiver.rstudio.com/" class="uri">https://vetiver.rstudio.com/</a>, pins <a href="https://pins.rstudio.com/" class="uri">https://pins.rstudio.com/</a>, plumber <a href="https://www.rplumber.io/" class="uri">https://www.rplumber.io/</a></p>
</div>
</center>
<aside class="notes">
<p>Development:</p>
<ul>
<li>Writing effective code</li>
<li>Connecting to data sources and systems</li>
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</section>
<section id="new-tools-and-tricks-sharing" class="slide level2 smaller">
<h2>New tools and tricks: Sharing</h2>
<div class="quarto-layout-panel">
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<p><img data-src="https://quarto.org/quarto.png" width="60"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>quarto</strong> - A new open-source scientific and technical publishing system that works with R, Python, Julia, Javascript, and many other languages.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
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<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>shinyuieditor</strong> - A visual tool for building the UI portion of a Shiny application that generates clean and human-readable code.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
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<p><img data-src="https://pkgs.rstudio.com/flexdashboard/reference/figures/logo.png" width="60"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>flexdashboard</strong> - Flexible and easy to specify row and column-based layouts. Components are intelligently re-sized to fill the browser and adapted for display on mobile devices.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://swag.rstudio.com/uploads/1/3/1/3/131335021/s815253891256106552_p6_i2_w660.png" width="60"></p>
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<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>rstudio/posit connect</strong> - Hosting for analytics, dashboards, API’s, pinned datasets while working in an enterprise environment.</p>
</div>
</div>
</div>
<center>
<div class="citation" style="font-size: 16px">
<p>quarto <a href="https://quarto.org/" class="uri">https://quarto.org/</a>, shinyuieditor <a href="https://rstudio.github.io/shinyuieditor/" class="uri">https://rstudio.github.io/shinyuieditor/</a>, flexdashboard <a href="https://pkgs.rstudio.com/flexdashboard/" class="uri">https://pkgs.rstudio.com/flexdashboard/</a>, Connect <a href="https://www.rstudio.com/products/connect/" class="uri">https://www.rstudio.com/products/connect/</a></p>
</div>
</center>
<aside class="notes">
<p>Sharing:</p>
<ul>
<li>Sharing outputs and securing access</li>
<li>Delivering actionable insights</li>
</ul>
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</section>
<section id="new-tools-and-tricks-productionize" class="slide level2 smaller">
<h2>New tools and tricks: Productionize</h2>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://git-scm.com/images/[email protected]" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>Version control</strong> - GitHub, Inc. is an Internet hosting service for software development and version control using Git. Other options include Bitbucket, Gitlab, and Azure DevOps.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://rstudio.github.io/renv/logo.svg" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>renv</strong> - renv helps manage library paths (and other project-specific state) to help isolate your project’s dependencies.</p>
</div>
</div>
</div>
<div class="quarto-layout-panel">
<div class="quarto-layout-row quarto-layout-valign-top">
<div class="quarto-layout-cell" style="flex-basis: 9.1%;justify-content: center;">
<p><img data-src="https://swag.rstudio.com/uploads/1/3/1/3/131335021/s815253891256106552_p6_i2_w660.png" width="70"></p>
</div>
<div class="quarto-layout-cell" style="flex-basis: 90.9%;justify-content: center;">
<p><strong>rstudio/posit package manager</strong> - In addition to providing standard mirrors of CRAN, Bioconductor, and PyPI, you can track changes over time or freeze packages to specific versions, to help ensure reproducibility and ease collaboration.</p>
</div>
</div>
</div>
<center>
<div class="citation" style="font-size: 16px">
<p>git <a href="https://git-scm.com/" class="uri">https://git-scm.com/</a>, renv <a href="https://rstudio.github.io/renv" class="uri">https://rstudio.github.io/renv</a>, Package Manager <a href="https://rstudio.com/products/package-manager/" class="uri">https://rstudio.com/products/package-manager/</a> and Public Package Manager <a href="https://packagemanager.rstudio.com/" class="uri">https://packagemanager.rstudio.com/</a></p>
</div>
</center>
<aside class="notes">
<p>Production:</p>
<ul>
<li>Code reproduceability</li>
<li>Managing packages and reproducing environments</li>
<li>Collaborating with team members</li>
<li>Implementing operational workflows and scaling</li>
</ul>
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</section>
<section id="environment-management-strategies" class="slide level2 smaller">
<h2>Environment Management Strategies</h2>
<p>Great data science work should be <strong>reproducible</strong> and <strong>collaborative</strong>.</p>
<p><img data-src="https://solutions.rstudio.com/environments/reproduce/reproducibility-strategies-and-danger-zones.png"></p>
<center>
<div class="citation" style="font-size: 16px">
<p>Environments Strategy Maps <a href="https://solutions.rstudio.com/environments/reproduce/" class="uri">https://solutions.rstudio.com/environments/reproduce/</a></p>
</div>
</center>
<aside class="notes">
<p>Being able to repeat experiments is the foundation of all science. Reproducing work is also critical for business applications: scheduled reporting, team collaboration, project validation.</p>
<p>Environment Management Strategies: - Snapshot and Restore - The snapshot and restore strategy fits when package access is open and users are responsible for reproducibility. - Shared Baseline - The shared baseline strategy fits when administrators or R champions are responsible for creating an environment where less experienced users can easily share and re-run work. - Validated - The validated strategy is similar to the shared baseline strategy. The main difference is the validated strategy targets teams wishing to restrict access to a particular set of packages and teams wishing to approve or audit changes to the package environment.</p>
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</section>
<section id="example-using-renv-git-and-public-package-manager" class="slide level2 smaller">
<h2>Example: Using renv, git, and Public Package Manager</h2>
<p><strong>Step 1: Use pre-compiled packages</strong></p>
<ul>
<li><p>Go to <a href="https://packagemanager.rstudio.com/client/#/">Public Package Manager</a></p></li>
<li><p>Click on <strong>Get Started</strong> -> <strong>Setup</strong> -> <strong>Distribution</strong> and select your OS -> Select <strong>Latest</strong> or <strong>Freeze</strong> and follow the instructions below the calendar.</p></li>
<li><p>For example:</p></li>
</ul>
<div class="sourceCode" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">options</span>(<span class="at">repos =</span> <span class="fu">c</span>(<span class="at">REPO_NAME =</span> <span class="st">"https://packagemanager.rstudio.com/all/latest"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<aside class="notes">
<p>Congratulations! You are now using hosted binary packages, no more struggling against c headers! to a particular set of packages and teams wishing to approve or audit changes to the package environment.</p>
<p>https://support.rstudio.com/hc/en-us/articles/360046703913-FAQ-for-RStudio-Public-Package-Manager</p>
<p>Package Manager supports users for accessing binaries of their packages. UI for searching through packages. Get information about it, crucially any system pre-requisites. If you need to grab an old version Package Manager hosts the old versions. Useful working with renv because if you need to restore a project that is older then likely it will need that older version. RStudio has a sync server where we take changes from CRAN and build the binaries. When you go to install a package we have binaries created. Fast, doesn’t need to be compiled from source. Useful for large packages like arrow (anything with system dependencies) to install quickly since it won’t need to build and prevent build failures.</p>
<p>We evaluate CRAN, Bioconductor, and PyPI each business day (Monday through Friday) and publish new snapshots when updates are available. Then, RStudio Public Package Manager syncs these snapshots daily. For example, suppose a CRAN package gets updated on Saturday. We will publish a new snapshot to the RStudio Package Service sometime on Monday, usually Monday afternoon. Then, the CRAN sync will pick up the change on Tuesday at 12:00 am. Occasionally, if there are very important updates, we generate an extra snapshot to make the updates available sooner. The timing of each snapshot varies based on the number of changes and the number of dependencies involved.</p>
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</section>
<section id="example-using-renv-git-and-public-package-manager-1" class="slide level2 smaller">
<h2>Example: Using renv, git, and Public Package Manager</h2>
<p><strong>Step 2: Use environment tracking</strong></p>
<div class="sourceCode" id="cb2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="fu">options</span>(<span class="at">repos =</span> <span class="fu">c</span>(<span class="at">REPO_NAME =</span> <span class="st">"https://packagemanager.rstudio.com/all/latest"</span>)) <span class="co"># We've already done this</span></span>
<span id="cb2-2"><a href="#cb2-2"></a></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="do">## Set up a new version controlled R project and install renv</span></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="fu">install.packages</span>(<span class="st">"renv"</span>)</span>
<span id="cb2-5"><a href="#cb2-5"></a><span class="fu">library</span>(renv)</span>
<span id="cb2-6"><a href="#cb2-6"></a></span>
<span id="cb2-7"><a href="#cb2-7"></a><span class="do">## Initialize your project with renv</span></span>
<span id="cb2-8"><a href="#cb2-8"></a>renv<span class="sc">::</span><span class="fu">init</span>()</span>
<span id="cb2-9"><a href="#cb2-9"></a></span>
<span id="cb2-10"><a href="#cb2-10"></a><span class="do">## After creating an R script and loading a couple libraries take a snapshot of the project </span></span>
<span id="cb2-11"><a href="#cb2-11"></a>renv<span class="sc">::</span><span class="fu">snapshot</span>()<span class="sc">:</span></span>
<span id="cb2-12"><a href="#cb2-12"></a></span>
<span id="cb2-13"><a href="#cb2-13"></a><span class="do">## Repeat a couple times, changing the packages being called so that we see something interesting when we run:</span></span>
<span id="cb2-14"><a href="#cb2-14"></a>renv<span class="sc">::</span><span class="fu">history</span>()</span>
<span id="cb2-15"><a href="#cb2-15"></a></span>
<span id="cb2-16"><a href="#cb2-16"></a><span class="do">## Optionally, revert back to an earlier snapshot:</span></span>
<span id="cb2-17"><a href="#cb2-17"></a>renv<span class="sc">::</span><span class="fu">revert</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<center>
<div class="citation" style="font-size: 16px">
<p>renv <a href="https://rstudio.github.io/renv" class="uri">https://rstudio.github.io/renv</a>, Package Manager <a href="https://rstudio.com/products/package-manager/" class="uri">https://rstudio.com/products/package-manager/</a> and Public Package Manager <a href="https://packagemanager.rstudio.com/" class="uri">https://packagemanager.rstudio.com/</a></p>
</div>
</center>
</section>
<section id="example-using-renv-git-and-public-package-manager-2" class="slide level2 smaller">
<h2>Example: Using renv, git, and Public Package Manager</h2>
<p><strong>Step 3: Easy collaboration</strong></p>
<div class="sourceCode" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="fu">options</span>(<span class="at">repos =</span> <span class="fu">c</span>(<span class="at">REPO_NAME =</span> <span class="st">"https://packagemanager.rstudio.com/all/latest"</span>)) <span class="co"># We've already done this</span></span>
<span id="cb3-2"><a href="#cb3-2"></a></span>
<span id="cb3-3"><a href="#cb3-3"></a><span class="do">## Send a colleague the link to your project on git, they'll restore your environment with:</span></span>
<span id="cb3-4"><a href="#cb3-4"></a>renv<span class="sc">::</span><span class="fu">restore</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<center>
<div class="citation" style="font-size: 16px">
<p>renv <a href="https://rstudio.github.io/renv" class="uri">https://rstudio.github.io/renv</a>, Package Manager <a href="https://rstudio.com/products/package-manager/" class="uri">https://rstudio.com/products/package-manager/</a> and Public Package Manager <a href="https://packagemanager.rstudio.com/" class="uri">https://packagemanager.rstudio.com/</a></p>
</div>
</center>
<aside class="notes">
<p>Congratulations! You now have a project that has all dependencies explicitly tracked. You can come back to this project weeks, years later and will be able to create exactly the environment it needs in order to successfully run with one command, renv::restore().</p>
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</section>
<section id="case-study" class="slide level2 smaller">
<h2>Case Study</h2>
<p><img data-src="https://github.com/sol-eng/bike_predict/raw/main/img/arrows.drawio.png" style="width:70.0%"></p>
<div class="citation" style="font-size: 16px">
<p>Bike Predict <a href="https://solutions.rstudio.com/example/bike_predict/" class="uri">https://solutions.rstudio.com/example/bike_predict/</a></p>
</div>
<aside class="notes">
<p>https://solutions.rstudio.com/example/bike_predict/</p>
<ul>
<li>Case Study
<ul>
<li>Bike predict</li>
<li>Workbench, Connect, Package Manager</li>
<li>Git version control and CI/CD</li>
<li>renv package management</li>
<li>Vetiver</li>
<li>Modularizing the code: API, Pins, Apps</li>
</ul></li>
</ul>
<style type="text/css">
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</section>
<section id="where-to-go-from-here" class="slide level2 smaller">
<h2>Where to go from here</h2>
<p><strong>What They Forgot to Teach You About R</strong> : <a href="https://rstats.wtf/" class="uri">https://rstats.wtf/</a></p>
<p><strong>Happy Git with R</strong> : <a href="https://happygitwithr.com/" class="uri">https://happygitwithr.com/</a></p>
<p><strong>Get started with renv in the RStudio IDE</strong>: <a href="https://docs.posit.co/ide/user/ide/guide/environments/r/renv.html" class="uri">https://docs.posit.co/ide/user/ide/guide/environments/r/renv.html</a></p>
<p><strong>Vetiver</strong></p>
<ul>
<li>Vetiver blog announcement post, <a href="https://www.rstudio.com/blog/announce-vetiver/" class="uri">https://www.rstudio.com/blog/announce-vetiver/</a></li>
<li>Vetiver tidyverse announcement post, <a href="https://www.tidyverse.org/blog/2022/06/announce-vetiver/" class="uri">https://www.tidyverse.org/blog/2022/06/announce-vetiver/</a></li>
</ul>
<p><strong>Using Public Package Manager</strong> : <a href="https://support.rstudio.com/hc/en-us/articles/360046703913-FAQ-for-RStudio-Public-Package-Manager" class="uri">https://support.rstudio.com/hc/en-us/articles/360046703913-FAQ-for-RStudio-Public-Package-Manager</a></p>
<p><strong>Interested in our Enterprise Products? Click <a href="https://www.rstudio.com/products/team/">here</a></strong></p>
<img src="images/posit-logo-black-TM.png" class="slide-logo r-stretch"><div class="footer footer-default">
<p><a href="http://solutions.rstudio.com/" class="uri">http://solutions.rstudio.com/</a></p>
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