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<p><strong>Last updated:</strong> 2018-10-31</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
<ul>
<li>
<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p>
<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
</details>
</li>
<li>
<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>Environment:</strong> empty </summary></p>
<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p>
</details>
</li>
<li>
<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>Seed:</strong> <code>set.seed(20181015)</code> </summary></p>
<p>The command <code>set.seed(20181015)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
</details>
</li>
<li>
<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>Session information:</strong> recorded </summary></p>
<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
</details>
</li>
<li>
<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/annakrystalli/rrtools-repro-research/tree/4d9cddb861a24119487c02587cd5f97b7ca19f68" target="_blank">4d9cddb</a> </summary></p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
<pre><code>
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: analysis/.DS_Store
Ignored: analysis/data/
Ignored: analysis/package.Rmd
Ignored: assets/
Ignored: docs/.DS_Store
Untracked files:
Untracked: docs/assets/Boettiger-2018-Ecology_Letters.pdf
Untracked: docs/assets/Packaging-Data-Analytical Work-Reproducibly-Using-R-and-Friends.pdf
Untracked: docs/css/
Untracked: libs/
</code></pre>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
</details>
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<details>
<summary> <small><strong>Expand here to see past versions:</strong></small> </summary>
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Rmd
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<td style="text-align:left;">
<a href="https://github.com/annakrystalli/rrtools-repro-research/blob/4d9cddb861a24119487c02587cd5f97b7ca19f68/analysis/index.Rmd" target="_blank">4d9cddb</a>
</td>
<td style="text-align:left;">
annakrystalli
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2018-10-31
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edit description
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Rmd
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<a href="https://github.com/annakrystalli/rrtools-repro-research/blob/8615159ac3e34d7f8ed56de74130b1671d77689b/analysis/index.Rmd" target="_blank">8615159</a>
</td>
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annakrystalli
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<td style="text-align:left;">
2018-10-30
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commit straglers
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<a href="https://cdn.rawgit.com/annakrystalli/rrtools-repro-research/8615159ac3e34d7f8ed56de74130b1671d77689b/docs/index.html" target="_blank">8615159</a>
</td>
<td style="text-align:left;">
annakrystalli
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<td style="text-align:left;">
2018-10-30
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commit straglers
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html
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<a href="https://cdn.rawgit.com/annakrystalli/rrtools-repro-research/921a7f864708008758ca207fa2761de380f22642/docs/index.html" target="_blank">921a7f8</a>
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annakrystalli
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2018-10-30
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annakrystalli
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2018-10-15
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update readme with NW R day details, add workshop index
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<a href="https://github.com/annakrystalli/rrtools-repro-research/blob/572d00b0a20ad9c41574091783ca726b85faa0b2/analysis/index.Rmd" target="_blank">572d00b</a>
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<td style="text-align:left;">
annakrystalli
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<td style="text-align:left;">
2018-10-15
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Start workflowr project.
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</ul>
</details>
<hr />
<div id="reproducible-research-in-r-with-rrtools" class="section level2">
<h2>Reproducible Research in R with <code>rrtools</code></h2>
<div id="st-october-northwest-universities-r-day" class="section level3">
<h3>31st October, Northwest Universities R Day</h3>
<hr />
<p><br></p>
</div>
</div>
<div id="workshop-outline" class="section level2">
<h2><strong>Workshop Outline</strong></h2>
<ul>
<li><h3 id="welcome"><a href="https://annakrystalli.me/rrtools-repro-research/intro.html"><strong>Welcome</strong></a></h3></li>
<li><h3 id="create-a-research-compendium"><a href="https://annakrystalli.me/rrtools-repro-research/create-compendium.html"><strong>Create a Research Compendium</strong></a></h3></li>
<li><h3 id="manage-functionality-as-a-package"><a href="https://annakrystalli.me/rrtools-repro-research/package.html"><strong>Manage functionality as a package</strong></a></h3></li>
<li><h3 id="reproduce-a-paper-in-rmd"><a href="https://annakrystalli.me/rrtools-repro-research/paper.html"><strong>Reproduce a paper in Rmd</strong></a></h3></li>
</ul>
<p><br></p>
<hr />
<div id="level" class="section level3">
<h3>Level</h3>
<p>Intermediate</p>
</div>
<div id="prerequisites" class="section level3">
<h3>Prerequisites:</h3>
<p>Familiarity with Version Control through RStudio and rmarkdown.</p>
</div>
<div id="system-requirements" class="section level3">
<h3>System Requirements:</h3>
<p>Pandoc (>= 1.17.2) LaTeX</p>
<p>If you don’t have LaTeX installed, consider installing <code>TinyTeX</code>, a custom LaTeX distribution based on TeX Live that is small in size but functions well in most cases, especially for R users.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">install.packages</span>(<span class="st">'tinytex'</span>)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2">tinytex<span class="op">::</span><span class="kw">install_tinytex</span>()</a></code></pre></div>
<p>Check <a href="https://yihui.name/tinytex/">docs</a> before before installing.</p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.19 digest_0.6.18
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] stringi_1.2.4 whisker_0.3-2 R.oo_1.21.0
[13] R.utils_2.6.0 rmarkdown_1.10 tools_3.4.4
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.4.4
[19] htmltools_0.3.6 knitr_1.20 </code></pre>
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