final build of website for 2019 course

computer_setup.Rmd

@@ -35,7 +35,7 @@ Much of the instruction below is from a great website set up by Jenny Bryan, cal
 
  1. **[Register for a free individual GitHub account](https://github.com/)** with your "`@ucdavis.edu`" email, and [request the Student Developer Pack](https://education.github.com/pack). This will give you unlimited private repositories, among other goodies. Do this ASAP! I think a human vets these requests, so don’t delay making this request. Think a little bit about your username and public profile, I suggest you use a real name and begin to build a scholarly identity in social media and coding, but it’s your decision.
 
- 2. Tell us your GitHub username using this [Google Form](https://goo.gl/forms/XDp7o1QNqz4JFgN03), so we can add you to the class Github Organization, **gge-ucd** (which is basically our own github "classroom"). We will set up a private repository for each student. So you just need the free individual account (i.e. we don’t have to wait for your Student Developer Pack to get approved).
+ 2. Tell us your GitHub username using this [Google Form](https://goo.gl/forms/SXgDhXguiijwOcQB2), so we can add you to the class Github Organization, **gge-ucd** (which is basically our own github "classroom"). We will set up a private repository for each student. So you just need the free individual account (i.e. we don’t have to wait for your Student Developer Pack to get approved).
 
  3. Please look for an invitation to join the [GGE-UCD Organization](https://github.com/gge-ucd) in your email. Once that's all done, we can create and add a private **repo**sitory that belongs only to you. Other students can see this repo, but they cannot edit it. The rest of the world cannot see it, only our class.
 

docs/assignments.html

@@ -502,14 +502,15 @@ <h4><strong>Part 1</strong></h4>
 <p>We will work in the same repository that you’ve been working in for the last couple of weeks: r-davis-in-class-YourName.</p>
 <p>For this homework, we are going to be working with a new dataset called <code>gapminder</code>. Download the data using the code below. Remember, this code is looking for a folder called <code>data</code> to put the .csv in, so make sure you have a folder named <code>data</code>, or modify the code to the correct folder name.</p>
 <pre class="r"><code>library(tidyverse)</code></pre>
-<pre><code>## ── Attaching packages ─────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
-<pre><code>## ✔ ggplot2 3.1.0.9000     ✔ purrr   0.3.0     
-## ✔ tibble  2.0.1          ✔ dplyr   0.8.0.1   
-## ✔ tidyr   0.8.2          ✔ stringr 1.4.0     
-## ✔ readr   1.3.1          ✔ forcats 0.3.0</code></pre>
-<pre><code>## ── Conflicts ────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+<pre><code>## ── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
+<pre><code>## ✔ ggplot2 3.1.0       ✔ purrr   0.3.1  
+## ✔ tibble  2.0.1       ✔ dplyr   0.8.0.1
+## ✔ tidyr   0.8.3       ✔ stringr 1.4.0  
+## ✔ readr   1.3.1       ✔ forcats 0.4.0</code></pre>
+<pre><code>## ── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ## ✖ dplyr::filter() masks stats::filter()
-## ✖ dplyr::lag()    masks stats::lag()</code></pre>
+## ✖ dplyr::lag()    masks stats::lag()
+## ✖ dplyr::n()      masks .env::n()</code></pre>
 <pre class="r"><code>gapminder &lt;- read_csv(&quot;https://gge-ucd.github.io/R-DAVIS/data/gapminder.csv&quot;)</code></pre>
 <pre><code>## Parsed with column specification:
 ## cols(

docs/computer_setup.html

@@ -553,7 +553,7 @@ <h2><code>Git</code> &amp; <strong>Github</strong> Account</h2>
 <p>Much of the instruction below is from a great website set up by Jenny Bryan, called <em>happygitwithr.com</em>.</p>
 <ol style="list-style-type: decimal">
 <li><p><strong><a href="https://github.com/">Register for a free individual GitHub account</a></strong> with your “<code>@ucdavis.edu</code>” email, and <a href="https://education.github.com/pack">request the Student Developer Pack</a>. This will give you unlimited private repositories, among other goodies. Do this ASAP! I think a human vets these requests, so don’t delay making this request. Think a little bit about your username and public profile, I suggest you use a real name and begin to build a scholarly identity in social media and coding, but it’s your decision.</p></li>
-<li><p>Tell us your GitHub username using this <a href="https://goo.gl/forms/XDp7o1QNqz4JFgN03">Google Form</a>, so we can add you to the class Github Organization, <strong>gge-ucd</strong> (which is basically our own github “classroom”). We will set up a private repository for each student. So you just need the free individual account (i.e. we don’t have to wait for your Student Developer Pack to get approved).</p></li>
+<li><p>Tell us your GitHub username using this <a href="https://goo.gl/forms/SXgDhXguiijwOcQB2">Google Form</a>, so we can add you to the class Github Organization, <strong>gge-ucd</strong> (which is basically our own github “classroom”). We will set up a private repository for each student. So you just need the free individual account (i.e. we don’t have to wait for your Student Developer Pack to get approved).</p></li>
 <li><p>Please look for an invitation to join the <a href="https://github.com/gge-ucd">GGE-UCD Organization</a> in your email. Once that’s all done, we can create and add a private <strong>repo</strong>sitory that belongs only to you. Other students can see this repo, but they cannot edit it. The rest of the world cannot see it, only our class.</p></li>
 <li><p>Setup <a href="http://happygitwithr.com/install-git.html"><strong>git</strong> on your computer</a>. The <strong>~</strong> is a shortcut, and it means your home directory (i.e., <strong>~</strong> = <code>/Users/myname</code> on a Mac, <strong>~</strong> = <code>C:/myname/Documents</code> on a PC).</p></li>
 </ol>

docs/index.html

@@ -528,7 +528,7 @@
 
 
 <h1 class="title toc-ignore">R-DAVIS</h1>
-<h4 class="date"><em>Updated: 2019-02-15</em></h4>
+<h4 class="date"><em>Updated: 2019-03-14</em></h4>
 
 </div>
 

docs/lesson_data_frames_continents.html

@@ -687,9 +687,9 @@ <h4 id="challenge-create-and-subset-a-vector">Challenge – Create and subset a
 <p>Similar to <code>c</code>, the <code>seq</code> function creates a vector: a <strong>seq</strong>uence of numbers.</p>
 <ul>
 <li><p>Your first task is to create a sequence of all the multiples of three from three to 300. Figure out how to do this. Some combination of playing with the function in the console and reading its helpfile (<code>?seq</code>) should work. Helpfiles are challenging at first, but it’s important to learn how to find the info you need in them. Hint: The arguments you need here are <code>from</code>, <code>to</code>, and <code>by</code>.</p></li>
-<li>Store your sequence in a variable.</li>
-<li>Extract the 33rd entry from the sequence</li>
-<li><strong>Bonus</strong>: Create a vector with ten evenly-spaced numbers starting with one and ending with one-million. What is the sum of the second and ninth entries in this vector?</li>
+<li><p>Store your sequence in a variable.</p></li>
+<li><p>Extract the 33rd entry from the sequence</p></li>
+<li><p><strong>Bonus</strong>: Create a vector with ten evenly-spaced numbers starting with one and ending with one-million. What is the sum of the second and ninth entries in this vector?</p></li>
 <li><p><strong>Super-Bonus</strong>: Returning to the multiples-of-three vector, what is the sum of the numbers in positions that are not evenly divisible by three? That is, the sum of the first, second, fourth, fifth, seventh, etc. entries.</p></li>
 </ul>
 </blockquote>

docs/lesson_data_frames_ecology.html

@@ -55512,7 +55512,7 @@ <h3 id="challenge-3">Challenge</h3>
           feel = c(&quot;furry&quot;, &quot;squishy&quot;, &quot;spiny&quot;),
           weight = c(45, 8 1.1, 0.8)
           )</code></pre></li>
-<li>Can you predict the class for each of the columns in the following example? Check your guesses using <code>str(country_climate)</code>:
+<li><p>Can you predict the class for each of the columns in the following example? Check your guesses using <code>str(country_climate)</code>:</p>
 <ul>
 <li>Are they what you expected? Why? Why not?</li>
 <li>What would have been different if we had added <code>stringsAsFactors = FALSE</code> when creating the data frame?</li>

docs/lesson_spreadsheets.html

@@ -972,7 +972,7 @@ <h2>A Note on Cross-platform Operability</h2>
 <p>thus causing terrible things to happen to your data. For example, <code>2\r</code> is not a valid integer, and thus will throw an error (if you’re lucky) when you attempt to operate on it in R or Python. Note that this happens on Excel for OSX as well as Windows, due to legacy Windows compatibility.</p>
 <p>There are a handful of solutions for enforcing uniform UNIX-style line endings on your exported CSV files:</p>
 <ol style="list-style-type: decimal">
-<li>When exporting from Excel, save as a “Windows comma separated (.csv)” file</li>
+<li><p>When exporting from Excel, save as a “Windows comma separated (.csv)” file</p></li>
 <li><p>If you store your data file under version control using Git, edit the <code>.git/config</code> file in your repository to automatically translate <code>\r\n</code> line endings into <code>\n</code>. Add the following to the file (<a href="http://nicercode.github.io/blog/2013-04-30-excel-and-line-endings">see the detailed tutorial</a>):</p>
 <pre><code> [filter &quot;cr&quot;]
      clean = LC_CTYPE=C awk &#39;{printf(\&quot;%s\\n\&quot;, $0)}&#39; | LC_CTYPE=C tr &#39;\\r&#39; &#39;\\n&#39;

docs/lesson_spreadsheets_condensed.html

@@ -557,129 +557,129 @@ <h1>Formatting</h1>
 <div id="avoiding-common-mistakes" class="section level1">
 <h1>Avoiding Common Mistakes</h1>
 <ul>
-<li>Avoid using multiple tables within one spreadsheet.</li>
-<li>Avoid spreading data across multiple tabs.
+<li><p>Avoid using multiple tables within one spreadsheet.</p></li>
+<li><p>Avoid spreading data across multiple tabs.</p>
 <ul>
 <li>Programs other than Excel will have a tough time seeing tabs</li>
 <li>Instead of adding a new tab, keep adding rows, and maybe use a new column for the info you’d be splitting across tabs. For example, use a column for Year instead of a new tab for a new year.</li>
 <li>If your table gets big, <a href="https://support.office.com/en-ca/article/Freeze-column-headings-for-easy-scrolling-57ccce0c-cf85-4725-9579-c5d13106ca6a">freeze your column headers</a> to make them easier to see while you scroll.</li>
 </ul></li>
-<li>Record zeros as zeros.
+<li><p>Record zeros as zeros.</p>
 <ul>
 <li>Zeros are data! Don’t use blanks, and don’t use zeros as null values</li>
 </ul></li>
-<li>Use an appropriate null value to record missing data.
+<li><p>Use an appropriate null value to record missing data.</p>
 <ul>
 <li>There’s a broader discussion of this in <a href="https://peerj.com/preprints/7/">White et al 2013</a>, but here’s a quick look at their recommendations:</li>
 </ul>
 <p><img src="figures/spreadsheet_fig/3_white_table_1.jpg" alt="White et al." /></p></li>
-<li>Don’t use formatting to convey information or to make your spreadsheet look pretty.
+<li><p>Don’t use formatting to convey information or to make your spreadsheet look pretty.</p>
 <ul>
 <li>R won’t see cell colors or bold fonts</li>
 <li>Keep data as characters or numbers</li>
 </ul></li>
-<li>Place comments in a separate column.
+<li><p>Place comments in a separate column.</p>
 <ul>
 <li>Don’t use Excel’s “comments” functionality, other programs don’t recognize these</li>
 <li>Just use a separate text column</li>
 </ul></li>
-<li>Record units in column headers.
+<li><p>Record units in column headers.</p>
 <ul>
 <li>Don’t put units in your data cells!</li>
 <li>10cm will be read as characters, not numbers</li>
 </ul></li>
-<li>Include only one piece of information in a cell.</li>
-<li>Avoid spaces, numbers and special characters in column headers.
+<li><p>Include only one piece of information in a cell.</p></li>
+<li><p>Avoid spaces, numbers and special characters in column headers.</p>
 <table align="center" style="width =80%; border: 1px solid black;">
 <tr>
 <td>
-<b>Good Name</b>
+<p><b>Good Name</b></p>
 </td>
-<br />
+<p><br /></p>
 <td>
-<b>Good Alternative </b>
+<p><b>Good Alternative </b></p>
 </td>
-<br />
+<p><br /></p>
 <td>
-<b>Avoid </b>
+<p><b>Avoid </b></p>
 </td>
-<br />
+<p><br /></p>
 </tr>
 <tr>
 <td>
-Max_temp_C
+<p>Max_temp_C</p>
 </td>
 <td>
-MaxTemp
+<p>MaxTemp</p>
 </td>
 <td>
-Maximum Temp (°C)
+<p>Maximum Temp (°C)</p>
 </td>
 </tr>
 <tr>
 <td>
-Precipitation_mm
+<p>Precipitation_mm</p>
 </td>
 <td>
-Precipitation
+<p>Precipitation</p>
 </td>
 <td>
-precmm
+<p>precmm</p>
 </td>
 </tr>
 <tr>
 <td>
-Mean_year_growth
+<p>Mean_year_growth</p>
 </td>
 <td>
-MeanYearGrowth
+<p>MeanYearGrowth</p>
 </td>
 <td>
-Mean growth/year
+<p>Mean growth/year</p>
 </td>
 </tr>
 <tr>
 <td>
-sex
+<p>sex</p>
 </td>
 <td>
-sex
+<p>sex</p>
 </td>
 <td>
-M/F
+<p>M/F</p>
 </td>
 </tr>
 <tr>
 <td>
-weight
+<p>weight</p>
 </td>
 <td>
-weight
+<p>weight</p>
 </td>
 <td>
-w.
+<p>w.</p>
 </td>
 </tr>
 <tr>
 <td>
-cell_type
+<p>cell_type</p>
 </td>
 <td>
-CellType
+<p>CellType</p>
 </td>
 <td>
-Cell Type
+<p>Cell Type</p>
 </td>
 </tr>
 <tr>
 <td>
-Observation_01
+<p>Observation_01</p>
 </td>
 <td>
-first_observation
+<p>first_observation</p>
 </td>
 <td>
-1st Obs
+<p>1st Obs</p>
 </td>
 </tr>
 </table></li>

docs/resources.html

@@ -446,7 +446,7 @@ <h3>Bonus Lessons</h3>
 <li><a href="lesson_ice_core_CO2_web_data.html">Pipelines: Download CO2 &amp; Ice Core Data &amp; Visualize</a></li>
 <li><a href="lesson_for_loops.html">For Loops</a></li>
 <li><a href="lesson_purrr_tutorial.html">Using purrr</a></li>
-<li><a href="https://ryanpeek.github.io/mapping_in_R/index.html">Mapping in R</a></li>
+<li><a href="https://ryanpeek.github.io/mapping-in-R-workshop/">Mapping in R</a></li>
 <li><a href="lesson_text_mining_mlk.html">Text Mining</a></li>
 <li><a href="lesson_github_collaboration.html">Github Collaboration with Branches</a></li>
 <li><a href="http://www.datacarpentry.org/R-ecology-lesson/05-r-and-databases.html">Data Carpentry: R and SQL</a></li>

docs/syllabus.html

@@ -631,7 +631,7 @@ <h4>Week 9</h4>
 <div id="week-10" class="section level4">
 <h4>Week 10</h4>
 <ul>
-<li>Students Choose!</li>
+<li><a href="https://ryanpeek.github.io/mapping-in-R-workshop/">Mapping in R</a></li>
 </ul>
 </div>
 </div>

setting_up_git.Rmd

@@ -53,14 +53,14 @@ For our purposes the "*best practice*" (i.e., **easier**) for setting up a new g
 
 ### 1. Create a New Repository on Github
 
- - Typically, the preferred method is to create a new repository on Github...*however*:
-    - *For our class, we are using a Github Classroom, which means we've already created the repository in advance and sent you a link. When you click the link, Github creates a new repository for you, which we as a class can all see and work with!*
+ - Typically, the preferred method is to create a new repository on Github...**HOWEVER**:
+ - For this class we've already created a repository for you, and you should have already gotten the link via email! When you click the link, Github creates a new repository for you, which our class will be able to view and work with!
 
 <br>
 
 ### 2. Clone Your Repository to your Computer
 
-You should now have a repository on github. Our class is all housed in the [gge-ucd](https://github.com/gge-ucd) Organization, so your repository should appear there, and it should look something like this:
+You should now have a repository on Github. Our class is all housed in the [gge-ucd](https://github.com/gge-ucd) Organization, so your repository should appear there, and it should look something like this:
 
   - [`https://github.com/gge-ucd/first_lastname`](https://github.com/gge-ucd/w01-fix-readme-ryanpeek). Take a minute to navigate to your repo online and take a look at your `README.md` file by clicking on it. 
   - **To _`clone`_ your repository** (*copy to your computer*):