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2020 updates
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177 changes: 145 additions & 32 deletions 00-course_info.Rmd
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Expand Up @@ -21,39 +21,43 @@ Students in ERHS 581A3 will meet for the first five weeks of the semester,
completing a one-credit course. Students in ERHS 581A4 will meet from the
sixth week to the final week of the semester, completing a two-credit course.

For the first five weeks of class, the course meets in the first-floor classroom
of the Military Sciences building on Mondays and Wednesdays, 10:00 am--11:50 am.
For the remaining weeks, the course meets in Room 120 of the Environmental
Health Building on Mondays and Wednesdays, 10:00 am--12:00 pm.
<!-- For the first five weeks of class, the course meets in the first-floor classroom -->
<!-- of the Military Sciences building on Mondays and Wednesdays, 10:00 am--11:50 am. -->
<!-- For the remaining weeks, the course meets in Room 120 of the Environmental -->
<!-- Health Building on Mondays and Wednesdays, 10:00 am--12:00 pm. -->

Exceptions to these meeting times are:
The course meets online. Course lectures are provided through YouTube videos. These
are embedded in the online course book, and the book also provides links to playlists
for each chapter of all the videos for that chapter.

- There will be no meeting on Labor Day (Monday, Sept. 2).
- There are no course meetings the week of Thanksgiving (week of Nov. 25).
- Office hours will be 10:00--11:00 AM on Fridays in EH 120.
Exceptions to the regular live meeting times are:

- There will be no meeting on Labor Day (Monday, Sept. 7).
- There are no course meetings the week of Thanksgiving (week of Nov. 23).
- Office hours will be 10:00--11:00 AM on Fridays on Zoom.

## Detailed schedule

Here is a more detailed view of the schedule for this course for Fall 2019:

```{r echo = FALSE}
a <- data.frame(week = 1:16,
date = c("Aug. 26, 28",
"Sept. 4",
"Sept. 9, 11",
"Sept. 16, 18",
"Sept. 23, 25",
"Sept. 30, Oct. 2",
"Oct. 7, 9",
"Oct. 14, 16",
"Oct. 21, 23",
"Oct. 28, 30",
"Nov. 4, 6",
"Nov. 11, 13",
"Nov. 18, 20",
"Dec. 2, 4",
"Dec. 9, 11",
"Week of Dec. 16"),
date = c("Aug. 24, 26",
"Aug. 31, Sept. 2",
"Sept. 9",
"Sept. 14, 16",
"Sept. 21, 23",
"Sept. 28, 30",
"Oct. 5, 7",
"Oct. 12, 14",
"Oct. 19, 21",
"Oct. 26, 28",
"Nov. 2, 4",
"Nov. 9, 11",
"Nov. 16, 18",
"Nov. 30, Dec. 2",
"Dec. 7, 9",
"Week of Dec. 14"),
level = c("Preliminary",
rep("Basic", 4),
rep("Intermediate", 4),
Expand All @@ -76,7 +80,7 @@ a <- data.frame(week = 1:16,
"Quiz (W)", "Quiz (W), HW #3 (F)",
"Quiz (W)", "Quiz (W), HW #4 (F)",
"", "HW #5 (F)",
"", "HW #6 (F)", "Project draft (M)",
"", "HW #6 (F)", "Project draft (W)",
"Final project"))
knitr::kable(a, col.names = c("Week", "Class dates", "Level", "Lecture content", "Graded items"))
```
Expand Down Expand Up @@ -133,7 +137,17 @@ knitr::kable(a, col.names = c("Assessment component",
### Attendance and class participation

Because so much of the learning for this class is through interactive work in
class, it is critical that you come to class.
class, it is critical that you attend the live Zoom sessions. Half of the class
will have these meetings from 10:00 AM--11:00 AM on Mondays and Wednesdays and the
other half will have these meetings from 11:00 AM--12:00 PM on Mondays and Wednesdays.

Videos of the lectures for each chapter of the online book will be shared through
YouTube. These will be embedded in the book, and a playlist for each chapter will
also be provided through a link at the start of that chapter in the book. You are
responsible for watching these videos before the in-person Zoom meetings. You will
get email reminders with a list of the videos that you need to watch before each
live Zoom meeting. There will be about two hours worth of video lectures each week, broken into
videos about 10--15 minutes each.

If you are in **ERHS 535**, out of a possible 10 points for class attendance,
you will get:
Expand All @@ -157,7 +171,7 @@ class attendance, you will get:

Exceptions:

- Attendance on the first day of class (Aug. 26) will not be counted.
- Attendance on the first day of class (Aug. 24) will not be counted.
- If you miss classes for "University-sanctioned" activities. These can include
attending a conference, travel to collect data for your dissertation), For these
absences, you must provide a signed letter from your research adviser. For more
Expand All @@ -169,15 +183,15 @@ if you bring in a note from a doctor of other medical professional giving the
date you missed and that it was for a serious medical issue.

**For an absence to be excused, you must email me a copy of the letter by 5:00 pm
the Friday afternoon of the week of the class you missed.**
the Friday afternoon following the class you missed.**

### Weekly in-course group exercises

Part of each class will be spent doing in-course group exercises. As long
The live Zoom meetings will be spent doing in-course group exercises. As long
as you are in class and participate in these exercises, you will get full credit
for this component.

**If you miss a class,** to get credit towards this component of your grade, you
**If you miss a live class meeting,** to get credit towards this component of your grade, you
will need to turn a few paragraphs describing what was covered in the exercise
and what you learned. To get credit for this, you must submit it to me by email
by 5:00 pm the Friday afternoon of the week of the class you missed.
Expand All @@ -191,6 +205,15 @@ There will be weekly in-course quizzes for weeks 2--10 of the course. Students
in ERHS 535 will take all these quizzes. Students in ERHS 581A3 will take
quizzes in weeks 2--5. Students in ERHS 581A4 will take quizzes in weeks 6--10.

Quizzes will be conducted through Google Forms. They will be immediately
graded, and you will get back your grade and feedback as soon as you submit
the quiz. All students will take the quizzes from 10:50 AM to 11:10 AM on
Wednesdays. Students in the 11:00 AM cohort should plan to arrive to the Zoom
meeting 10 minutes early on Wednesdays.

You must stay on Zoom while you complete the quiz. A link to the quiz will be
provided at 10:50 AM in the Zoom chat.

Each quiz will have at least 10 questions. Typically, a quiz will have more
questions, usually 12--15 questions. The grading of the quizzes is structures
so that you can get full credit for the quiz portion of the grade without
Expand Down Expand Up @@ -306,7 +329,7 @@ You will do the final group project in groups of 4. The final product will be a
<!-- - [Should Travelers Avoid Flying Airlines That Have Had Crashes in the Past?](http://fivethirtyeight.com/features/should-travelers-avoid-flying-airlines-that-have-had-crashes-in-the-past/) -->
<!-- - [Billion-Dollar Billy Beane](http://fivethirtyeight.com/features/billion-dollar-billy-beane/) -->

You will have in-class group work time to work on this. This project will also require some work with your group outside of class. You will be able to get feedback from me through weekly informal written reports in these weeks. I will also provide feedback and help during the in-class group work time.
You will have in-class group work time to work on this on Zoom. This project will also require some work with your group outside of class. I will provide feedback and help during the in-class group work time on Zoom.

The final group project will be graded with A through F, with the following point values (out of 30 possible):

Expand Down Expand Up @@ -388,7 +411,8 @@ cover about a chapter of the book each week of the course.

This coursebook includes:

- Links to the slides presented in class for each topic
- Embedded video lectures for the course
- Links to the slides presented in video lectures for each topic
- In-course exercises, typically including links to the data used in the exercise
- An appendix with homework assignments
- A list of vocabulary and concepts that should be mastered for each quiz
Expand Down Expand Up @@ -429,3 +453,92 @@ statistics and bioinformatics. If you are using R for a specific type of
analysis, you will be able to find many books with advice on using R for both
general and specific statistical analysis, including many available in print or
online through the CSU library.

## In-course Exercise Chapter 0

Today, we'll practice doing an in-course exercise, including using breakout groups in
Zoom and rotating sharing screens. The purpose of this in-course exercise is to let
us all try out how breakout groups and a remote "pair programming" approach to
working on the in-course exercises will work. Also, the prompts in this exercise
will help you explore the online book and videos for this class to make sure that
you are comfortable with navigating those resources.

You will work on this for 20 minutes. At the end of this
time, please re-join the large Zoom meeting that we started in.

For each of the three sections below, pick one group member to share his or her
screen in Zoom in your breakout group. That person should do try the following
steps. If you are the person sharing your screen, talk through what you're
trying out and why you're trying different things. If you are not sharing your
screen, add suggestions as the other group member tries this, especially if he
or she gets stuck at some point.

The last prompt requires you to have RStudio installed. If someone in your group
has this installed, save that person's turn for last. If nobody in the group
has RStudio installed, you can read through this part without doing the activities.

### Navigate the online course book

Pick one group member to share his or her screen in Zoom in your breakout group.

Find the following in the book:

- The schedule for this course, including the dates that homeworks are due and the dates that quizzes will be given
- Information on the grading policies for quizzes for this course
- You have your first quiz Wednesday, September 2. What are the vocabulary terms you will be responsible for in the first quiz?
- You will have your first homework assignment due Friday, September 11.
+ How many homeworks are due in total over the full semester (for those taking ERHS 535)?
+ When is the second homework due?
+ Find the assignment information for the first homework in the course book.
+ How will you turn in your first homework?
- Find information on the requirements for "Course set-up" from the chapter on
course information. Click on the links for downloading R and RStudio. Make sure
everyone in the group sees where they will need to go to download R and RStudio.
You will need to do this before the class meeting on Wednesday.

### Find the video lectures

Pick a different group member to share his or her screen in Zoom in your
breakout group.

- Look through the book to find links to the YouTube video lectures for Chapter 1 ("R Preliminaries"). You should be able to find:
+ Embedded videos throughout the text
+ Links to download the pdfs for each video below each embedded video
+ A link to a YouTube playlist with all the video lectures for the chapter at the beginning of the chapter text.
- Download the pdf copy of the slides for the first video lecture for Chapter 1.
- Watch the beginning of the first video lecture for Chapter 1.
- You will need to watch the first nine video lectures for Chapter 1 before we
meet on Wednesday.
+ What are the titles of these nine videos?
+ What is the title of the only video for Chapter 1 that you are **not** required to watch before Wednesday's meeting?

### Try coding a bit

Pick a different group member to share his or her screen in Zoom in your
breakout group. Pick someone who already has RStudio installed, if possible.

- Open RStudio
- Open an R script by going to "File" -> "New File" -> "R Script"
- Type the following code in the R script:

```{r eval = FALSE}
sample(c("Johnny", "Waylon", "Willie", "Kris"))
```

- Highlight the code you just typed and then click the "Run" bottom on the top right
of the script file. Look in the "Console" pane of RStudio. What output do you see?
- In the script, replace each name with the name of a member of your group. Re-run the
code by highlighting it again and the pressing the "Run" button. What output do you see
in the console?
- Without changing the code, highlight and run it three more times. Is the output the
same each time?
- Click your cursor in the R script pane and then save this R script by going to
"File" -> "Save". Save the file somewhere that's easy to find, like on your Desktop
(you can delete it after today). Save it with the name "example.R".
- Send this file to your other group members through Zoom chat as a file attachment.
When you use Chat in Zoom, you should see a button for "File". This should allow you
to select and send the R script you just saved.
- Have another group member share their screen and then open this file in RStudio
(open RStudio, and then go to "File" -> "Open File" and select the file from where
you saved it in your computer). Try highlighting and running this code on this computer.

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