Merge pull request #85 from earthlab/dev-lessons

Dev lessons merge into  dev

Author: Leah Wasser

README.md

@@ -44,4 +44,11 @@ bundle exec jekyll serve
 ## Build Notes:
 
 * the site requires jekyll flavored markdown. Be sure to specify that if you are knitting.
-* in rmd files - be sure to specify fig.cap="text here" to add alt text to any code chunks that output a FIGURE. 
+* in rmd files - be sure to specify fig.cap="text here" to add alt text to any code chunks that output a FIGURE.
+
+## CSS
+
+Currently, we are using less. to install less
+
+1. install nodejs (npm) https://nodejs.org/en/
+2. install less : `sudo npm install less -g` NOTE: you need administration access to install 

_config.yml

@@ -137,7 +137,7 @@ kramdown:
   auto_ids: true
   footnote_nr: 1
   entity_output: as_char
-  toc_levels: 1..6
+  toc_levels: 1..3
   smart_quotes: lsquo,rsquo,ldquo,rdquo
   enable_coderay: false
 

_data/navigation.yml

@@ -43,11 +43,11 @@ earth-analytics-2017:
         url: /course-materials/earth-analytics/
       - title: "Syllabus"
         url: /course-materials/earth-analytics/earth-analytics-syllabus/
-  - title: "WK 1-3: Intro to R & Disturbance"
+  - title: "Course Weeks 1-3"
     children:
-      - title: "Wk 1: Introduction "
+      - title: "Week 1: Getting Started With Data"
         url: /course-materials/earth-analytics/week-1/
-      - title: "Wk 2: Flood Data in R "
+      - title: "Week 2: Time Series Data in R"
         url: /course-materials/earth-analytics/week-2/
-      - title: "Wk 3: Lidar Data in R"
+      - title: "Week 3: Lidar Data in R"
         url: /course-materials/earth-analytics/week-3/

_events/courses/2017-01-17-earth-analytics-course.md

@@ -11,18 +11,18 @@ header:
   cta_url:
   overlay_filter: rgba(0, 0, 0, 0.5)
   caption:
-excerpt: 'Earth Analytics Spring 2017 - Fuse data science skills with Earth system science knowledge.'
+excerpt: 'Earth Analytics Spring 2017 - Fuse Data Science Skills with Earth System Science Knowledge.'
 sidebar:
   nav: earth-analytics-2017
 startTime: '3:00'
 endTime: '17:50'
 ---
 
-## About
+## Earth Analytics Course Home
 
 This advanced, multidisciplinary course will address major questions in Earth
 science and teach students to use the analytical tools necessary to undertake
-exploration of ‘big scientific data’. If you are a graduate and undergraduate
+exploration of ‘big scientific data’. If you are a graduate or undergraduate
 (junior/senior) student in the natural/social science disciplines with an
 interest in learning about computationally intensive science, this
 course is for you.
@@ -36,13 +36,13 @@ course is for you.
 * **Teaching Assistant:** Sepideh Khanghah
 * **Time:** Wednesday 3:00 pm -  5:50 pm
 * **Location:** SEEC S125
-* **Sections:** GEOG 4100-001 (Junior / Senior Level undergraduate), GEOG 5100-003 (Graduate)
+* **Sections:** GEOG 4563 (Junior / Senior Level undergraduate), GEOG 5563 (Graduate)
 
 Please direct questions to Leah Wasser (leah.wasser at colorado.edu).
 
 </div>
 
-### Example Course Science Topics (Topics subject to change):
+### Example Science Topics:
 
 * **Climate & Disturbance (Fire / Drought / Permafrost):** How
 changing climate impacts natural disturbance systems.

_includes/class_navigation.html

@@ -0,0 +1,64 @@
+
+
+
+
+
+<nav class="nav__list">
+  <ul>
+    <li><span class="nav__sub-title"><i class="fa fa-book" aria-hidden="true"></i> {{ page.class-lesson |  replace: '-',' ' |  replace: '"',' ' |  remove: ']' |  remove: '['}} Lessons</span>
+      <ul>
+        {% assign sorted_posts = site.posts | sort:"order" %}
+        {% for post in sorted_posts %}
+          {% if post.class-lesson == page.class-lesson %}
+            {% if post.url == page.url %}
+            <li><a href= {{ site.url }}{{ site.baseurl }}{{ post.url }} class='active'>{{ post.order }}. {{ post.nav-title }}</a></li>
+            {% else %}
+            <li><a href= {{ site.url }}{{ site.baseurl }}{{ post.url }}>{{ post.order }}. {{ post.nav-title }}</a></li>
+            {% endif %}
+          {% endif %}
+        {% endfor %}
+      </ul>
+    </li>
+  </ul>
+<!-- slide list will only render if there are slideshows associated with a lesson series -->
+        {% for slides in site.slide-shows %}
+          {% if slides.class-lesson == page.class-lesson %}
+          {% if forloop.first %}
+          <ul>
+            <li><span class="nav__sub-title">Slide Shows</span>
+              <ul>
+          {% endif %}
+            <li><a href="{{ site.url }}{{ site.baseurl }}{{ slides.url}}" target='_blank'>{{ slides.title }} </a></li>
+            {% endif %}
+          {% if forloop.last %}
+              </ul>
+            </li>
+          </ul>
+          {% endif %}
+        {% endfor %}
+<!-- end slideshows  -->
+</nav>
+
+<h3>Other Week {{ page.week }} Lessons</h3>
+
+{% assign modules = site.posts | where:"order", 1 %}
+{% assign weeks = modules | where:"week", page.week %}
+
+{% for module in weeks %}
+{% if module.class-lesson != page.class-lesson %}
+<nav class="nav__list">
+<a href="{{ site.url }}{{ module.permalink }}">
+  <ul>
+    <li><span class="nav__sub-title grey"><i class="fa fa-book" aria-hidden="true"></i> {{ module.module-title |  replace: '-',' ' |  replace: '"',' ' |  remove: ']' |  remove: '['}} Lessons</span>
+    </ul></a>
+</nav>
+{% endif %}
+{% endfor %}
+
+<!-- Only add this if the page has a week asociated with it -->
+{% if page.week %}
+{% capture the_path %}{{ site.url }}/course-materials/earth-analytics/week-{{ page.week }}/{% endcapture %}
+
+<a href="{{ the_path }}" ><i class="fa fa-arrow-circle-left"></i> Return to week {{ page.week }}</a>
+
+{% endif %}

_includes/class_navigation_week.html

@@ -0,0 +1,84 @@
+{% assign sorted_posts = site.posts | sort:"order" %}
+<!--<h3>Week {{ page.week }} Lessons</h3>-->
+
+{% assign modules = site.posts | where:"order", 1 %}
+
+{% assign weeks = sorted_posts | where:"week", page.week %}
+
+{% assign classes = weeks | where:"module-type", 'class' %}
+{% assign homework = weeks | where:"module-type", 'homework' %}
+
+{% if page.week %}
+  {% capture the_path %}{{ site.url }}/course-materials/earth-analytics/week-{{ page.week }}/{% endcapture %}
+  <h4><a href="{{ the_path }}" ><i class="fa fa-home" aria-hidden="true"></i> Week {{ page.week }}</a></h4>
+{% endif %}
+<nav class="nav__list">
+  <ul>
+    <li><span class="nav__sub-title"><i class="fa fa-folder-open" aria-hidden="true"></i> In Class Materials</span>
+      <ul>
+        {% for module in classes %}
+        {% if module.order == 1 %}
+            {% assign class_lessons = weeks | where:"class-lesson", module.class-lesson %}
+            <li><span class="nav__sub-title grey"><i class="fa fa-book" aria-hidden="true"></i> {{ module.module-nav-title | capitalize }} </span></li>
+        {% endif %}
+
+        <ul>
+        {% for alesson in class_lessons %}
+          {% if alesson.url == page.url %}
+          <li><a href= {{ site.url }}{{ alesson.url }} class='active'>{{ alesson.order }}. {{ alesson.nav-title }}</a></li>
+          {% else %}
+          <li><a href= {{ site.url }}{{ alesson.url }}>{{ alesson.order }}. {{ alesson.nav-title }}</a></li>
+          {% endif %}
+        {% endfor %}
+       </ul>
+        {% endfor %}
+       </ul>
+
+   <li><span class="nav__sub-title"><i class="fa fa-folder-open" aria-hidden="true"></i> Homework Materials</span>
+     <ul>
+       {% for module in homework %}
+       {% if module.order == 1 %}
+           {% assign class_lessons = weeks | where:"class-lesson", module.class-lesson %}
+           <li><i class="fa fa-book" aria-hidden="true"></i> {{ module.module-nav-title }} </li>
+       {% endif %}
+
+       <ul>
+       {% for alesson in class_lessons %}
+         {% if alesson.url == page.url %}
+         <li><a href= {{ site.url }}{{ alesson.url }} class='active'>{{ alesson.order }}. {{ alesson.nav-title }}</a></li>
+         {% else %}
+         <li><a href= {{ site.url }}{{ alesson.url }}>{{ alesson.order }}. {{ alesson.nav-title }}</a></li>
+         {% endif %}
+       {% endfor %}
+        </ul>
+       {% endfor %}
+     </ul>
+   </ul>
+</nav>
+
+
+{% if page.week %}
+  {% if page.week > 1 and page.week <= 4 %}
+  <hr>
+   {% assign previousWeek = page.week | minus: 1 %}
+   {% capture previous_week_path %}{{ site.url }}/course-materials/earth-analytics/week-{{ previousWeek }}/{% endcapture %}
+   <h5><a href="{{ previous_week_path }}" ><i class="fa fa-arrow-circle-left"></i> {{ previousWeek }} </a>
+   go to week
+   {% endif %}
+
+
+   {% if page.week == 1 %}
+    {% assign nextWeek = page.week | plus: 1 %}
+    {% capture next_week_path %}{{ site.url }}/course-materials/earth-analytics/week-{{ nextWeek }}/{% endcapture %}
+    <h5>go to week<a href="{{ next_week_path }}" > {{ nextWeek }} <i class="fa fa-arrow-circle-right"></i> </a></h5>
+    {% endif %}
+ {% if page.week >= 2 and page.week <= 3 %}
+  {% assign nextWeek = page.week | plus: 1 %}
+  {% capture next_week_path %}{{ site.url }}/course-materials/earth-analytics/week-{{ nextWeek }}/{% endcapture %}
+
+  <a href="{{ next_week_path }}" > {{ nextWeek }} <i class="fa fa-arrow-circle-right"></i> </a></h5>
+  {% endif %}
+
+{% endif %}
+
+<h5><a href="{{ site.url }}/course-materials/earth-analytics/" ><i class="fa fa-home" aria-hidden="true"></i> Course Home</a></h5>

_includes/earth-analytics/homework-wk1.md

@@ -0,0 +1,122 @@
+<!-- start homework activity -->
+
+
+<div class="notice--warning" markdown="1">
+
+## <i class="fa fa-pencil-square-o" aria-hidden="true"></i> Homework Submission: Create A Report Using Knitr & RMarkdown
+
+* Create a new rmarkdown `.Rmd` file in `Rstudio`. Name the file:
+`yourLastName-firstInitial-week1.Rmd` example: `wasser-l-week1.Rmd`
+
+* Add an `author:` line to the `YAML` header at the top of your `.Rmd` document.
+* Give your file an appropriate title. Suggestion: `Earth Analytics Spring 2017: Homework - Week 1`
+* At the top of the rmarkdown document (BELOW THE YAML HEADER), add some text
+that describes:
+
+   * What an `.Rmd` file is
+   * How you can use `knitr` in `R` and what it does.
+   * Why using `Rmarkdown` to create reports can be helpful to both you and your colleagues that you work with on a project.
+
+* Create a new CODE CHUNK
+* Copy and paste the code BELOW into the code chunk that you just created.
+* Below the code chunk in your `rmarkdown` document, add some TEXT that describes what the plot that you created
+shows - interpret what you see in the data.
+* Finally, in your own words, summarize what you think the plot shows / tells us about
+the flood and also how the data that produced the plot were likely collected. Use the video
+about the Boulder Floods as a reference when you write this summery.
+
+BONUS: If you know `R`, clean up the plot by adding labels and a title. Or better
+yet, use `ggplot2`!
+
+</div>
+
+
+```r
+
+# load the ggplot2 library for plotting
+library(ggplot2)
+
+# download data from figshare
+# note that we are downloaded the data into your
+download.file(url = "https://ndownloader.figshare.com/files/7010681",
+              destfile = "data/boulder-precip.csv")
+
+# import data
+boulder.precip <- read.csv(file="data/boulder-precip.csv")
+
+# view first few rows of the data
+head(boulder.precip)
+
+# when we download the data we create a dataframe
+# view each column of the data frame using it's name (or header)
+boulder.precip$DATE
+
+# view the precip column
+boulder.precip$PRECIP
+
+# q plot stands for quick plot. Let's use it to plot our data
+qplot(x=boulder.precip$DATE,
+      y=boulder.precip$PRECIP)
+
+```
+
+<figure class="half">
+<a href="/images/rfigs/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd05-knitr/render-plot-1.png">
+<img src="/images/rfigs/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd05-knitr/render-plot-1.png" alt="example of the plot">
+</a>
+<figcaption>
+If your code ran properly, the resulting plot should look like this one.
+</figcaption>
+</figure>
+
+
+<figure>
+<a href="/images/course-materials/earth-analytics/week-1/setup-r-rstudio/r-markdown-wk-1.png">
+<img src="/images/course-materials/earth-analytics/week-1/setup-r-rstudio/r-markdown-wk-1.png" alt="R markdown example image.">
+</a>
+<figcaption>
+Your rmarkdown file should look something like the one above (with your own text
+added to it). Note that the imaglocalhoste above is CROPPED at the bottom. Your rmarkdown
+file will have more code in it.
+</figcaption>
+</figure>
+
+### Troubleshooting: missing plot
+
+If the code above did not produce a plot, please check the following:
+
+#### Check your working directory
+
+If the path to your file is not correct, then the data won't load into `R`.
+If the data don't load into `R`, then you can't work with it or plot it.
+
+To figure out your current working directory use the command: `getwd()`
+Next, go to your finder or file explorer on your computer. Navigate to the path
+that `R` gives you when you type `getwd()` in the console. It will look something
+like the path example: `/Users/your-username/documents/earth-analytics`
+
+```r
+# check your working directory
+getwd()
+
+## [1] "/Users/lewa8222/documents/earth-analytics"
+```
+
+In the example above, note that my USER directory is called `lewa8222`. Yours
+is called something different. Is there a `data` directory within the earth-analytics
+directory?
+
+<figure>
+<a href="/images/course-materials/earth-analytics/week-1/setup-r-rstudio/data-dir-wk-1.png">
+<img src="/images/course-materials/earth-analytics/week-1/setup-r-rstudio/data-dir-wk-1.png" alt="data directory example image.">
+</a>
+<figcaption>
+Your working directory should contain a `/data` directory.
+</figcaption>
+</figure>
+
+If not, review the [working directory lesson](/course-materials/earth-analytics/week-1/setup-working-directory/)
+to ensure your working directory is SETUP properly on your computer and in `RStudio`.
+
+
+<!-- end homework activity -->

_includes/lesson-pagination.html

@@ -2,6 +2,9 @@
 <!-- NOTE: it won't include slideshows as written which makes sense -->
 <!-- add forced pagination -->
 <!-- first, get total lesson count -->
+
+<div class="previous--next">
+
 {% assign counter = 0 %}
 {% for post in site.categories.course-materials %}
     {% if post.class-lesson == page.class-lesson %}
@@ -18,14 +21,15 @@
       {% if post.order == prevPageNum %}
         <a href="{{ site.url }}{{ site.baseurl }}{{ post.url }}" class="btn btn--info btn--large btn-success">
           <i class="fa fa-4 fa-arrow-circle-left fa-4" aria-hidden="true"></i>
-          PREVIOUS - {{ post.nav-title }} </a>
+          {{ post.nav-title }} </a>
       {% endif %}
 
       {% assign nextPageNum = page.order | plus: 1 %}
       {% if post.order == nextPageNum %}
        <a href="{{ site.url }}{{ site.baseurl }}{{ post.url }}" class="btn btn--info btn--large btn-success" style="float:right" >
-         {{ post.nav-title }} - NEXT
+         {{ post.nav-title }}
          <i class="fa fa-4 fa-arrow-circle-right" aria-hidden="true"></i></a>
       {% endif %}
     {% endif %}
 {% endfor %}
+</div>