<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="author" content="Robert Schlegel" />
<meta name="date" content="2019-03-19" />
<title>Best practices</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.0.13/css/fa-svg-with-js.css" rel="stylesheet" />
<script src="site_libs/font-awesome-5.0.13/js/fontawesome-all.min.js"></script>
<script src="site_libs/font-awesome-5.0.13/js/fa-v4-shims.min.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2,h3",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = true;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
padding-left: 25px;
text-indent: 0;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Detecting marine heatwaves from imperfect data</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="about.html">About</a>
</li>
<li>
<a href="license.html">License</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Vignettes
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="r_vs_python.html">Python vs. R - default outputs</a>
</li>
<li>
<a href="r_vs_python_arguments.html">Python vs. R - default arguments</a>
</li>
<li>
<a href="r_vs_python_additional.html">Python vs. R - additional functions</a>
</li>
<li>
<a href="Short_climatologies.html">Short climatologies</a>
</li>
<li>
<a href="Climatologies_and_baselines.html">Alternative climatologies and baselines</a>
</li>
<li>
<a href="time_series_duration.html">Effects of short time series</a>
</li>
<li>
<a href="missing_data.html">Effects of missing data</a>
</li>
<li>
<a href="gridded_products.html">Difference between gridded products</a>
</li>
<li>
<a href="best_practices.html">Best practices</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/robwschlegel/MHWdetection">
<span class="fa fa-github"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<!-- Add a small amount of space between sections. -->
<style type="text/css">
div.section {
padding-top: 12px;
}
</style>
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Best practices</h1>
<h4 class="author"><em>Robert Schlegel</em></h4>
<h4 class="date"><em>2019-03-19</em></h4>
</div>
<p><strong>Last updated:</strong> 2019-03-19</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
<ul>
<li>
<p><details> <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>
<p><details> <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>
<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Seed:</strong> <code>set.seed(666)</code> </summary></p>
<p>The command <code>set.seed(666)</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>
<p><details> <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>
<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/robwschlegel/MHWdetection/tree/970b22c7c2cae4e09824722f8bf1d87fb5118a73" target="_blank">970b22c</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: .Rhistory
Ignored: .Rproj.user/
Ignored: data/sst_ALL_clim_only.Rdata
Ignored: data/sst_ALL_event_aov_tukey.Rdata
Ignored: data/sst_ALL_flat.Rdata
Ignored: data/sst_ALL_miss.Rdata
Ignored: data/sst_ALL_miss_cat_chi.Rdata
Ignored: data/sst_ALL_miss_clim_event_cat.Rdata
Ignored: data/sst_ALL_miss_clim_only.Rdata
Ignored: data/sst_ALL_miss_event_aov_tukey.Rdata
Ignored: data/sst_ALL_repl.Rdata
Ignored: data/sst_ALL_smooth.Rdata
Ignored: data/sst_ALL_smooth_aov_tukey.Rdata
Ignored: data/sst_ALL_smooth_event.Rdata
Ignored: data/sst_ALL_trend.Rdata
Ignored: data/sst_ALL_trend_clim_event_cat.Rdata
Untracked files:
Untracked: analysis/bibliography.bib
Untracked: code/functions.R
Untracked: code/workflow.R
Untracked: data/.gitignore
Untracked: data/clim_py.csv
Untracked: data/clim_py_joinAG_1.csv
Untracked: data/clim_py_joinAG_5.csv
Untracked: data/clim_py_joinAG_no.csv
Untracked: data/clim_py_minD_3.csv
Untracked: data/clim_py_minD_7.csv
Untracked: data/clim_py_pctile_80.csv
Untracked: data/clim_py_pctile_95.csv
Untracked: data/clim_py_pctile_99.csv
Untracked: data/clim_py_random.csv
Untracked: data/clim_py_spw_11.csv
Untracked: data/clim_py_spw_51.csv
Untracked: data/clim_py_spw_no.csv
Untracked: data/clim_py_whw_3.csv
Untracked: data/clim_py_whw_7.csv
Untracked: data/mhwBlock.csv
Untracked: data/mhws_py.csv
Untracked: data/mhws_py_joinAG_1.csv
Untracked: data/mhws_py_joinAG_5.csv
Untracked: data/mhws_py_joinAG_no.csv
Untracked: data/mhws_py_minD_3.csv
Untracked: data/mhws_py_minD_7.csv
Untracked: data/mhws_py_pctile_80.csv
Untracked: data/mhws_py_pctile_95.csv
Untracked: data/mhws_py_pctile_99.csv
Untracked: data/mhws_py_random.csv
Untracked: data/mhws_py_spw_11.csv
Untracked: data/mhws_py_spw_51.csv
Untracked: data/mhws_py_spw_no.csv
Untracked: data/mhws_py_whw_3.csv
Untracked: data/mhws_py_whw_7.csv
Untracked: data/sst_ALL.Rdata
Untracked: data/sst_ALL_KS.Rdata
Untracked: data/sst_ALL_cat_chi.Rdata
Untracked: data/sst_ALL_clim_category_count.Rdata
Untracked: data/sst_ALL_con.Rdata
Untracked: data/sst_ALL_detrend.Rdata
Untracked: data/sst_ALL_event_cor.Rdata
Untracked: data/sst_ALL_miss_clim_KS_p.Rdata
Untracked: data/sst_ALL_miss_clim_aov_p.Rdata
Untracked: data/sst_ALL_miss_clim_aov_tukey.Rdata
Untracked: data/sst_ALL_miss_event_CI.Rdata
Untracked: data/sst_ALL_smooth_R2.Rdata
Untracked: data/sst_ALL_smooth_R2_base.Rdata
Untracked: data/sst_ALL_smooth_cor_base.Rdata
Untracked: data/sst_ALL_smooth_real_category.Rdata
Untracked: data/sst_ALL_trend_cat_chi.Rdata
Untracked: data/sst_ALL_trend_clim_KS_p.Rdata
Untracked: data/sst_ALL_trend_clim_aov_tukey.Rdata
Untracked: data/sst_ALL_trend_clim_only.Rdata
Untracked: data/sst_ALL_trend_event_CI.Rdata
Untracked: data/sst_ALL_trend_event_aov_tukey.Rdata
Untracked: data/sst_WA.csv
Untracked: data/sst_WA_miss_ice.csv
Untracked: data/sst_WA_miss_random.csv
Unstaged changes:
Deleted: .Rbuildignore
Modified: .gitignore
Deleted: DESCRIPTION
Deleted: NAMESPACE
Modified: NEWS.md
Deleted: R/MHWdetection-package.R
Deleted: R/placeholder.R
Modified: README.md
Deleted: _pkgdown.yml
Modified: _workflowr.yml
Modified: analysis/_site.yml
Deleted: docs/articles/fig/heatwaveR_v3.svg
Deleted: docs/docsearch.css
Deleted: docs/docsearch.js
Deleted: docs/link.svg
Deleted: docs/pkgdown.css
Deleted: docs/pkgdown.js
Deleted: docs/pkgdown.yml
Deleted: docs/sitemap.xml
Deleted: man/MHWdetection-package.Rd
Deleted: man/placeholder.Rd
Deleted: tests/testthat.R
Deleted: tests/testthat/test-placeholder.R
Deleted: vignettes/.gitignore
Deleted: vignettes/Climatologies_and_baselines.Rmd
Deleted: vignettes/Short_climatologies.Rmd
Deleted: vignettes/best_practices.Rmd
Deleted: vignettes/bibliography.bib
Deleted: vignettes/data/.gitignore
Deleted: vignettes/data/clim_py.csv
Deleted: vignettes/data/clim_py_joinAG_1.csv
Deleted: vignettes/data/clim_py_joinAG_5.csv
Deleted: vignettes/data/clim_py_joinAG_no.csv
Deleted: vignettes/data/clim_py_minD_3.csv
Deleted: vignettes/data/clim_py_minD_7.csv
Deleted: vignettes/data/clim_py_pctile_80.csv
Deleted: vignettes/data/clim_py_pctile_95.csv
Deleted: vignettes/data/clim_py_pctile_99.csv
Deleted: vignettes/data/clim_py_random.csv
Deleted: vignettes/data/clim_py_spw_11.csv
Deleted: vignettes/data/clim_py_spw_51.csv
Deleted: vignettes/data/clim_py_spw_no.csv
Deleted: vignettes/data/clim_py_whw_3.csv
Deleted: vignettes/data/clim_py_whw_7.csv
Deleted: vignettes/data/mhwBlock.csv
Deleted: vignettes/data/mhws_py.csv
Deleted: vignettes/data/mhws_py_joinAG_1.csv
Deleted: vignettes/data/mhws_py_joinAG_5.csv
Deleted: vignettes/data/mhws_py_joinAG_no.csv
Deleted: vignettes/data/mhws_py_minD_3.csv
Deleted: vignettes/data/mhws_py_minD_7.csv
Deleted: vignettes/data/mhws_py_pctile_80.csv
Deleted: vignettes/data/mhws_py_pctile_95.csv
Deleted: vignettes/data/mhws_py_pctile_99.csv
Deleted: vignettes/data/mhws_py_random.csv
Deleted: vignettes/data/mhws_py_spw_11.csv
Deleted: vignettes/data/mhws_py_spw_51.csv
Deleted: vignettes/data/mhws_py_spw_no.csv
Deleted: vignettes/data/mhws_py_whw_3.csv
Deleted: vignettes/data/mhws_py_whw_7.csv
Deleted: vignettes/data/sst_ALL.Rdata
Deleted: vignettes/data/sst_ALL_KS.Rdata
Deleted: vignettes/data/sst_ALL_cat_chi.Rdata
Deleted: vignettes/data/sst_ALL_clim_category_count.Rdata
Deleted: vignettes/data/sst_ALL_con.Rdata
Deleted: vignettes/data/sst_ALL_detrend.Rdata
Deleted: vignettes/data/sst_ALL_event_cor.Rdata
Deleted: vignettes/data/sst_ALL_miss_clim_KS_p.Rdata
Deleted: vignettes/data/sst_ALL_miss_clim_aov_p.Rdata
Deleted: vignettes/data/sst_ALL_miss_clim_aov_tukey.Rdata
Deleted: vignettes/data/sst_ALL_miss_event_CI.Rdata
Deleted: vignettes/data/sst_ALL_miss_event_aov_tukey.Rdata
Deleted: vignettes/data/sst_ALL_smooth_R2.Rdata
Deleted: vignettes/data/sst_ALL_smooth_R2_base.Rdata
Deleted: vignettes/data/sst_ALL_smooth_cor_base.Rdata
Deleted: vignettes/data/sst_ALL_smooth_real_category.Rdata
Deleted: vignettes/data/sst_ALL_trend_cat_chi.Rdata
Deleted: vignettes/data/sst_ALL_trend_clim_KS_p.Rdata
Deleted: vignettes/data/sst_ALL_trend_clim_aov_tukey.Rdata
Deleted: vignettes/data/sst_ALL_trend_clim_only.Rdata
Deleted: vignettes/data/sst_ALL_trend_event_CI.Rdata
Deleted: vignettes/data/sst_ALL_trend_event_aov_tukey.Rdata
Deleted: vignettes/data/sst_WA.csv
Deleted: vignettes/data/sst_WA_miss_ice.csv
Deleted: vignettes/data/sst_WA_miss_random.csv
Deleted: vignettes/fig/detect_diagram.svg
Deleted: vignettes/fig/heatwaveR_v3.svg
Deleted: vignettes/gridded_products.Rmd
Deleted: vignettes/missing_data.Rmd
Deleted: vignettes/r_vs_python.Rmd
Deleted: vignettes/r_vs_python_additional.Rmd
Deleted: vignettes/r_vs_python_arguments.Rmd
Deleted: vignettes/time_series_duration.Rmd
Deleted: vignettes/trend.Rmd
Deleted: vignettes/variance.Rmd
</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>
</li>
</ul>
<details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary>
<ul>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
File
</th>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
<th style="text-align:left;">
Message
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/robwschlegel/MHWdetection/blob/970b22c7c2cae4e09824722f8bf1d87fb5118a73/analysis/best_practices.Rmd" target="_blank">970b22c</a>
</td>
<td style="text-align:left;">
robwschlegel
</td>
<td style="text-align:left;">
2019-03-19
</td>
<td style="text-align:left;">
Publish the vignettes from when this was a pkgdown framework
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/robwschlegel/MHWdetection/fa7fd57d97caa42308afbb27f761077d74e5239e/docs/best_practices.html" target="_blank">fa7fd57</a>
</td>
<td style="text-align:left;">
robwschlegel
</td>
<td style="text-align:left;">
2019-03-19
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/robwschlegel/MHWdetection/blob/64ac134076a04088c834291ce86c6405eedaf672/analysis/best_practices.Rmd" target="_blank">64ac134</a>
</td>
<td style="text-align:left;">
robwschlegel
</td>
<td style="text-align:left;">
2019-03-19
</td>
<td style="text-align:left;">
Publish analysis files
</td>
</tr>
</tbody>
</table>
</ul>
<p></details></p>
<hr />
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>In this vignette the results from the main three vignettes are combined in order to visualise them simultaneously. Following this are individual sections on how to address the challenges presented by length, missing data, and decadal trends respectively.</p>
</div>
<div id="overview-of-reference-time-series" class="section level2">
<h2>Overview of reference time series</h2>
<pre class="r"><code># A multi-panel summary figure with images and tables
load("data/sst_ALL.Rdata")
# sst_ALL_summary <- sst_ALL %>%
# Poential panels
# 1) The base time series
# 1.1) Rug pplot showing events
# 1.2) Events filled in with flames
# 1.3) Overlay thresholds
# 1.4) Overlay category thresholds
# 2) Mini map showing pixel location
# 3) Stats table (showing relevant stats for/from best practices)
# 4) The climatolgies/categories as there own doy x-axis panel
# 5) Lolli plot showing events
# ggplot(sst_ALL_summary)</code></pre>
</div>
<div id="overview-of-results" class="section level2">
<h2>Overview of results</h2>
<p>The following figures show the combined results from time series length, missing data, and decadal trends side by side for each of the three components of the results. This helps to create a more complete pictures of the importance of the different variables.</p>
<div id="climatologies" class="section level3">
<h3>Climatologies</h3>
</div>
<div id="event-metrics" class="section level3">
<h3>Event metrics</h3>
</div>
<div id="category-counts" class="section level3">
<h3>Category counts</h3>
<div id="refs">
</div>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.18 digest_0.6.16
[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_1.22.0
[13] R.utils_2.7.0 rmarkdown_1.10 tools_3.5.3
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.5.3
[19] htmltools_0.3.6 knitr_1.20 </code></pre>
</div>
<!-- Adjust MathJax settings so that all math formulae are shown using
TeX fonts only; see
http://docs.mathjax.org/en/latest/configuration.html. This will make
the presentation more consistent at the cost of the webpage sometimes
taking slightly longer to load. Note that this only works because the
footer is added to webpages before the MathJax javascript. -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
"HTML-CSS": { availableFonts: ["TeX"] }
});
</script>
<hr>
<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a>
analysis was created with
<a href="https://github.com/jdblischak/workflowr">workflowr</a> 1.1.1
</p>
<hr>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>