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docs/outline.html

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@@ -511,33 +511,31 @@ <h3>Cache Credentials</h3>
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<div id="https-configure-rrstudio-to-work-with-your-gitgithub" class="section level4">
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<h4>HTTPS: Configure R/RStudio to work with your Git/GitHub</h4>
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<p>For most new Git users, the following steps are the most convenient and efficient for configuring your new applications for Git version control. <strong>If</strong> you use <strong>two-factor</strong> authentication with <strong>GitHub</strong>, skip the the SSH section below.</p>
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<p>In your RStudio Console…. (<a href="http://keziamanlove.com/wp-content/uploads/2013/10/RStudioScreenshot1_Inkscape.png">image</a>)</p>
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<ol style="list-style-type: decimal">
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<li><p>In your RStudio Console, install the <code>usethis</code> package. If you have not installed a package before, this <a href="https://tutorials.shinyapps.io/00-setup/#section-install-packages">brief install package videos</a> is helpful.</p>
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<ol style="list-style-type: lower-alpha">
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<li>Install the <code>usethis</code> package</li>
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<li>Install the <code>usethis</code> package. (If you have not installed a <strong>package</strong> before, this <a href="https://tutorials.shinyapps.io/00-setup/#section-install-packages">brief install package videos</a> is helpful)</li>
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<li><p>Load the <code>usethis</code> package:</p>
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<ol style="list-style-type: decimal">
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<ol style="list-style-type: lower-alpha">
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<li><code>library(usethis)</code></li>
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<li>(Video: <a href="https://youtu.be/3RWb5U3X-T8?t=159">Example of loading a libraryin the RStudio console</a>)</li>
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</ol></li>
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<li><p>In the RStudio <strong>console</strong>, configure <code>usethis</code> You will <strong>need to follow the instructions from within the console</strong>, after invoking the <code>use_usethis</code> function:</p>
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<ol style="list-style-type: decimal">
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<ol style="list-style-type: lower-alpha">
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<li><code>use_usethis()</code></li>
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<li>Restart R</li>
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</ol></li>
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<li><p>Configure your Git client with <a href="https://github.com/settings/emails">your GitHub email address</a></p>
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<ol style="list-style-type: decimal">
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<ol style="list-style-type: lower-alpha">
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<li><code>library(usethis)</code></li>
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<li><code>use_git_config(user.name = &quot;&lt;&lt;github ID&gt;&gt;&quot;, user.email = &quot;&lt;&lt;my github associated email address&gt;&gt;&quot;)</code></li>
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<li>For example: <code>use_git_config(user.name = &quot;libjohn&quot;, user.email = &quot;libjohn@duke.edu&quot;)</code></li>
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</ol></li>
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<li><p>Generate a GitHub Personal Access Token (PAT) and associate that token within your RStudio Environment (<code>.Renviron</code>). Do this by running the following command <strong>in the RStudio console</strong> and following all the prompts. When you run the command, below, this will spawn a GitHub Page that generates a PAT. Copy the PAT into your clipboard buffer. Paste the PAT into RStudio’s editor window for the <code>.Renviron</code> file. the PAT is your personal token; do not share it. You can do all this by invoking the <code>browse_github_pat</code> fuction in the RStudio Console and following the resulting console prompts. If you need more detail, see the <a href="https://usethis.r-lib.org/articles/articles/usethis-setup.html">usethis Setup</a> instructions.</p>
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<ol style="list-style-type: decimal">
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<li>usethis::browse_github_pat()</li>
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<ol style="list-style-type: lower-alpha">
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<li><code>browse_github_pat()</code></li>
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<li>The RStudio Console will direct you how to <code>edit_r_environ()</code> in the RStudio Editor window</li>
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<li>Restart R</li>
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</ol></li>
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</ol></li>
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</ol>
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<p>Let’s assume you did everything correctly. Now you’re ready go to the <a href="handson.html">Hands-On</a> section which we will cover in the workshop.</p>
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<hr />

outline.Rmd

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For most new Git users, the following steps are the most convenient and efficient for configuring your new applications for Git version control. **If** you use **two-factor** authentication with **GitHub**, skip the the SSH section below.
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1. In your RStudio Console, install the `usethis` package. If you have not installed a package before, this [brief install package videos](https://tutorials.shinyapps.io/00-setup/#section-install-packages) is helpful.
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In your RStudio Console.... ([image](http://keziamanlove.com/wp-content/uploads/2013/10/RStudioScreenshot1_Inkscape.png))
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a. Install the `usethis` package
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a. Load the `usethis` package:
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1. `library(usethis)`
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1. (Video: [Example of loading a libraryin the RStudio console](https://youtu.be/3RWb5U3X-T8?t=159))
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1. Install the `usethis` package. (If you have not installed a **package** before, this [brief install package videos](https://tutorials.shinyapps.io/00-setup/#section-install-packages) is helpful)
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1. Load the `usethis` package:
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a. `library(usethis)`
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a. (Video: [Example of loading a libraryin the RStudio console](https://youtu.be/3RWb5U3X-T8?t=159))
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a. In the RStudio **console**, configure `usethis` You will **need to follow the instructions from within the console**, after invoking the `use_usethis` function:
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1. In the RStudio **console**, configure `usethis` You will **need to follow the instructions from within the console**, after invoking the `use_usethis` function:
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1. `use_usethis()`
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1. Restart R
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a. Configure your Git client with [your GitHub email address](https://github.com/settings/emails)
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a. `use_usethis()`
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a. Restart R
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1. `library(usethis)`
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1. `use_git_config(user.name = "<<github ID>>", user.email = "<<my github associated email address>>")`
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1. For example: `use_git_config(user.name = "libjohn", user.email = "libjohn@duke.edu")`
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1. Configure your Git client with [your GitHub email address](https://github.com/settings/emails)
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a. Generate a GitHub Personal Access Token (PAT) and associate that token within your RStudio Environment (`.Renviron`). Do this by running the following command **in the RStudio console** and following all the prompts. When you run the command, below, this will spawn a GitHub Page that generates a PAT. Copy the PAT into your clipboard buffer. Paste the PAT into RStudio's editor window for the `.Renviron` file. the PAT is your personal token; do not share it. You can do all this by invoking the `browse_github_pat` fuction in the RStudio Console and following the resulting console prompts. If you need more detail, see the [usethis Setup](https://usethis.r-lib.org/articles/articles/usethis-setup.html) instructions.
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a. `library(usethis)`
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a. `use_git_config(user.name = "<<github ID>>", user.email = "<<my github associated email address>>")`
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a. For example: `use_git_config(user.name = "libjohn", user.email = "libjohn@duke.edu")`
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1. usethis::browse_github_pat()
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1. The RStudio Console will direct you how to `edit_r_environ()` in the RStudio Editor window
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1. Restart R
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1. Generate a GitHub Personal Access Token (PAT) and associate that token within your RStudio Environment (`.Renviron`). Do this by running the following command **in the RStudio console** and following all the prompts. When you run the command, below, this will spawn a GitHub Page that generates a PAT. Copy the PAT into your clipboard buffer. Paste the PAT into RStudio's editor window for the `.Renviron` file. the PAT is your personal token; do not share it. You can do all this by invoking the `browse_github_pat` fuction in the RStudio Console and following the resulting console prompts. If you need more detail, see the [usethis Setup](https://usethis.r-lib.org/articles/articles/usethis-setup.html) instructions.
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a. `browse_github_pat()`
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a. The RStudio Console will direct you how to `edit_r_environ()` in the RStudio Editor window
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a. Restart R
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Let's assume you did everything correctly. Now you're ready go to the [Hands-On](handson.html) section which we will cover in the workshop.

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