updates to course materials

Leah Wasser · Leah Wasser · commit d518ea10d1a2 · 2017-01-13T11:24:10.000-07:00
diff --git a/_posts/course-materials/earth-analytics/2016-12-06-geog-4563-5563-syllabus.md b/_posts/course-materials/earth-analytics/2016-12-06-geog-4563-5563-syllabus.md
@@ -1,36 +1,47 @@
 ---
+title: 'GEOG 4563 & 5563 - Earth Analytics: Spring 2017 Syllabus'
+authors: Leah Wasser
+category: course-materials
+output: pdf_document
+excerpt: .
 layout: single
-title: "GEOG 4563 & 5563 - Earth Analytics: Spring 2017 Syllabus"
-excerpt: "."
-authors: ['Leah Wasser']
-category: [course-materials]
+nav-title: Course Syllabus
+comments: no
 permalink: /course-materials/earth-analytics/earth-analytics-syllabus/
-nav-title: 'Course Syllabus'
 sidebar:
   nav: earth-analytics-2017
-author_profile: false
-comments: false
+author_profile: no
 ---
 
 
 ## Lead Instructor
 
 Dr. Leah A Wasser
-Office. S346 SEEC
-Ph. 303.735.4637
-leah.wasser@colorado.edu
+
+Office. S346 SEEC * Ph. 303.735.4637 * leah.wasser@colorado.edu
+
+## Teaching Assistant
+Sepideh Dadashi
+email: seda8302@colorado.edu
 
 <div class='notice--success' markdown="1">
 
-# Where & When
+## Where & When
 
-* **Teaching Assistant:** Sepideh Khanghah
+* **Teaching Assistant:** Sepideh Dadashi
 * **Time:** Wednesday 3:00 pm -  5:50 pm
 * **Location:** SEEC S125
 
-**Contributing Instructors:**
+## Office Hours
+
+* Mondays: 1:00pm-3:00pm, Leah Wasser SEEC Earth Lab - S346
+* Tuesdays: 1:00pm - 3:00pm, Sepideh Dadashi, SEEC Earth Lab main space S348
+
+
+<a href="{{ site.url }}/pdf/course-materials/earth-analytics/2016-12-06-geog-4163-5163-syllabus.pdf" class="btn btn-success btn--x-large">
+<i class="fa fa-download" aria-hidden="true"></i> course syllabus (.pdf)</a>
+</div>
 
-  </div>
 
 ## About the Course
 This advanced, multidisciplinary course will address major questions in Earth
diff --git a/_posts/course-materials/earth-analytics/week-1/co-floods-1-intro/2016-12-06-erosion-02-precip-discharge-r-example.md b/_posts/course-materials/earth-analytics/week-1/co-floods-1-intro/2016-12-06-erosion-02-precip-discharge-r-example.md
@@ -3,7 +3,7 @@ layout: single
 title: "Work with Precipitation Data in R - 2013 Colorado Floods"
 excerpt: "This lesson provides students wiht an example of a data driven report to emphsize the importance of connecting data, documentation and results."
 authors: ['Leah Wasser', 'NEON Data Skills', 'Mariela Perignon']
-modified: 2017-01-12
+modified: 2017-01-13
 category: [course-materials]
 class-lesson: ['co-floods-1-intro']
 permalink: /course-materials/earth-analytics/week-1/co-floods-data-example-r/
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd01-why-rmarkdown.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd01-why-rmarkdown.md
@@ -8,7 +8,7 @@ class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/intro-rmarkdown-knitr/
 nav-title: 'Intro to R Markdown'
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 module-title: 'Document & Publish a Workflow with R Markdown & Knitr'
 module-nav-title: 'R Markdown Intro'
 module-description: 'This module teaches participants how to use R Markdown
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd02-RMarkdown.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd02-RMarkdown.md
@@ -4,7 +4,7 @@ title: "Write Reports and Document Workflow Using R Markdown"
 excerpt: 'This tutorial cover how to create an R Markdown file in R and then
 render it to html using knitr.'
 authors: [Leah Wasser, NEON Data Skills]
-modified: 2017-01-12
+modified: 2017-01-13
 category: [course-materials]
 class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/intro-rmarkdown-knitr2/
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd03-markdown.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd03-markdown.md
@@ -4,7 +4,7 @@ title: "Intro to Markdown"
 excerpt: 'This tutorial cover how to use Markdown syntax in R and then
 render it to html using knitr.'
 authors: [Leah Wasser, NEON Data Skills]
-modified: 2017-01-12
+modified: 2017-01-13
 category: [course-materials]
 class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/intro-to-markdown/
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd04-intro-to-code-chunks.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd04-intro-to-code-chunks.md
@@ -6,7 +6,7 @@ R Markdown file in R Studio. It also explores how to use comments to document yo
 code workflow.'
 authors: [Leah Wasser, NEON Data Skills]
 category: [course-materials]
-modified: 2017-01-12
+modified: 2017-01-13
 class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/code-chunks-comments-knitr/
 nav-title: 'Code Chunks'
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd05-knitr.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd05-knitr.md
@@ -5,7 +5,7 @@ description: "This tutorial introduces how to use the R knitr package to publish
 from R Markdown files to HTML (or other) file format."
 authors: ['Leah Wasser', 'NEON Data Skills']
 category: [course-materials]
-modified: 2017-01-12
+modified: 2017-01-13
 class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/knit-rmarkdown-document-to-pdf/
 nav-title: 'Knit .Rmd to .html'
diff --git a/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd06-Setup-Resources.md b/_posts/course-materials/earth-analytics/week-1/intro-knitr-rmd/2016-12-06-Rmd06-Setup-Resources.md
@@ -5,7 +5,7 @@ excerpt: "This lesson contains a list of resources that will help you work with
 R markdown. If you know of other resources, please add them to the comments
 below."
 authors: ['Leah Wasser']
-modified: 2017-01-12
+modified: 2017-01-13
 category: [course-materials]
 class-lesson: ['intro-rmarkdown-knitr']
 permalink: /course-materials/earth-analytics/week-1/intro-rmarkdown-knitr6/
diff --git a/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-01-r-rstudio.md b/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-01-r-rstudio.md
@@ -6,7 +6,7 @@ title: 'Install & setup R and RStudio on your laptop'
 attribution: 'These materials were adapted from Software Carpentry materials by Earth Lab.'
 excerpt: 'This tutorial walks you through downloading and installing R and RStudio on your computer.'
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 module-title: 'Setup R, RStudio & Your Working Directory'
 module-description: 'This module walks you through getting R and RStudio setup on your
 laptop. It also introduces file organization strategies.'
diff --git a/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-02-rstudio-overview.md b/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-02-rstudio-overview.md
@@ -6,7 +6,7 @@ title: 'Get to Know RStudio'
 attribution: 'These materials were adapted from Software Carpentry materials by Earth Lab.'
 excerpt: 'This tutorial walks you through downloading and installing R and RStudio on your computer.'
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 nav-title: 'RStudio Intro'
 week: 1
 sidebar:
diff --git a/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-03-packages.md b/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-03-packages.md
@@ -6,7 +6,7 @@ title: 'Install & Use Packages in R'
 attribution: 'These materials were adapted from Software Carpentry materials by Earth Lab.'
 excerpt: 'Packages are sets of functions that perform tasks that help us work with various data structures in R. This tutorial walks you through installing and loading R packages R in RStudio.'
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 nav-title: 'Install Packages'
 week: 1
 sidebar:
diff --git a/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-04-file-organization-101.md b/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-04-file-organization-101.md
@@ -11,7 +11,7 @@ sidebar:
 class-lesson: ['setup-r-rstudio']
 permalink: course-materials/earth-analytics/week-1/file-organization-101/
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 course: 'earth-analytics'
 author_profile: false
 comments: true
diff --git a/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-05-working-directory.md b/_posts/course-materials/earth-analytics/week-1/setup-r-rstudio/2016-12-08-setup-05-working-directory.md
@@ -13,7 +13,7 @@ sidebar:
 class-lesson: ['setup-r-rstudio']
 permalink: course-materials/earth-analytics/week-1/setup-working-directory/
 dateCreated: 2016-12-12
-modified: 2017-01-12
+modified: 2017-01-13
 author_profile: false
 comments: true
 order: 5
diff --git a/_posts/course-materials/earth-analytics/week-3/lidar-intro/2016-12-06-raster03-lidar-raster-data.md b/_posts/course-materials/earth-analytics/week-3/lidar-intro/2016-12-06-raster03-lidar-raster-data.md
@@ -3,7 +3,7 @@ layout: single
 title: "Introduction to lidar raster data products"
 excerpt: "This lesson reviews how a lidar data point cloud is converted to a raster."
 authors: ['Leah Wasser', 'NEON Data Skills']
-modified: 2017-01-12
+lastModified: 2017-01-13
 category: [course-materials]
 class-lesson: ['class-lidar-r']
 permalink: /course-materials/earth-analytics/week-3/lidar-raster-data/
@@ -12,7 +12,7 @@ week: 3
 sidebar:
   nav:
 author_profile: false
-comments: true
+comments: false
 order: 3
 ---
 {% include toc title="In This Lesson" icon="file-text" %}
@@ -27,7 +27,7 @@ After completing this tutorial, you will be able to:
 * Describe the basic process of how a lidar point cloud is converted into a raster.
 * Be able to describe the structural differences between a raster dataset and a lidar point cloud.
 
-## <i class="fa fa-check-square-o fa-2" aria-hidden="true"></i> What you need
+## <i class="fa fa-check-square-o fa-2" aria-hidden="true"></i> What You Need
 
 You will need a computer with internet access to complete this lesson.
 
@@ -111,7 +111,7 @@ recorded by the sensor.
    </figcaption>
 </figure>
 
-## Create A Raster From LiDAR Point Clouds
+## Creating A Raster From LiDAR Point Clouds
 
 There are different ways to create a raster from LiDAR point clouds. Let's look
 at one of the most basic ways to create a raster file points - gridding.
@@ -160,12 +160,6 @@ To work with raster data in `R`, we can use the `raster` and `rgdal` packages.
 
 # load libraries
 library(raster)
-## Loading required package: sp
-## 
-## Attaching package: 'raster'
-## The following object is masked from 'package:dplyr':
-## 
-##     select
 library(rgdal)
 ## rgdal: version: 1.2-4, (SVN revision 643)
 ##  Geospatial Data Abstraction Library extensions to R successfully loaded
@@ -179,9 +173,9 @@ library(rgdal)
 # setwd("working-dir-path-here")
 ```
 
-We can use the `raster()` function to open a raster in `R`. The raster() function
-has one required argument: the path to the raster that you want to open. So you'd
-use it as follows: raster("path-to-raster-here").
+We can use the `raster("path-to-raster-here")` function to open a raster in R.
+
+## NOTE SWITCH THIS TO USE THE DEM INSTEAD.
 
 
 ```r
@@ -246,7 +240,7 @@ are in meters. We won't get into too much detail about coordinate refence string
 in this class but they are important to be familiar with when working with spatial
 data.
 
-### Distribution of elevation values
+## Distribution of elevation values
 
 We can view the distribution of elevation values in our data too. This is useful
 for identifying outlier data values.
diff --git a/org/earth-analytics/week-1.md b/org/earth-analytics/week-1.md
@@ -27,9 +27,9 @@ document and convert it to a pdf using `knitr`.
 ## <i class="fa fa-pencil"></i> Homework Week 1
 
 ### 1. Readings
-Five selfish reasons to work reproducibly - Florian Markowetz
+* [Five selfish reasons to work reproducibly - Florian Markowetz](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0850-7)
 
-Computing Workflows for Biologists: A Roadmap
+* Computing Workflows for Biologists: A Roadmap
 
 
 ### 2. Watch Flood Video
@@ -62,7 +62,7 @@ ALL of the lessons and have your computer setup BEFORE class begins next week.
 You will be behind if these things are not setup / complete before week 2.
 {: .notice }
 
-### 4. Complete assignment below
+### 5. Complete assignment below
 
 After you have reviewed the lessons above, complete the assignment below.
 Submit your `.pdf` document and R markdown document to ... by **Tuesday 23
diff --git a/processing-code/knitRMD-2-MD-all-new-files.R b/processing-code/knitRMD-2-MD-all-new-files.R
@@ -154,7 +154,7 @@ all_rmd_files <- as.data.frame(list.files(file.path(git_repo_base_path, repo_pos
                                           recursive = T, full.names = T))
 names(all_rmd_files) <- "rmd_files"
 
-all_rmd_files_bld <- populate_all_rmd_df(all_rmd_files, all=T)
+all_rmd_files_bld <- populate_all_rmd_df(all_rmd_files, all=F)
 
 # just one file
 # create_markdown(all_rmd_files_bld[20, ], wd)
