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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
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<title>Syllabus</title>
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<a class="navbar-brand" href="index.html">Intro to R</a>
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<ul class="nav navbar-nav">
<li>
<a href="syllabus.html">Syllabus</a>
</li>
<li>
<a href="materials_schedule.html">Materials + Schedule</a>
</li>
<li>
<a href="resources.html">Resources</a>
</li>
<li>
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<h1 class="title toc-ignore">Syllabus</h1>
</div>
<p><br></p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p><strong>Epi/Biostats Summer Institute - Introduction to R for Public
Health Researchers 140.604.73</strong></p>
<p>This course will provide <em>“hands-on” training</em> for learning
how to analyze data in the R statistical software package. We will cover
data input/output, data management and manipulation, and how to make
useful and informative graphics.</p>
<p><br></p>
</div>
<div id="objectives" class="section level2">
<h2>Objectives</h2>
<p>By the end of the course, students should be comfortable:</p>
<ul>
<li>Reading data into R</li>
<li>Recoding and manipulating data</li>
<li>Using R add-on packages</li>
<li>Making exploratory plots</li>
<li>Performing basic statistical tests</li>
<li>Understanding basic programming syntax</li>
<li>Creating reproducible R documents</li>
</ul>
<p><br></p>
</div>
<div id="logistics" class="section level2">
<h2>Logistics</h2>
<p><br></p>
<div id="when" class="section level3">
<h3>When</h3>
<ul>
<li><strong>Dates:</strong> June 10-14, 17-18, and 20-21, 2024 (In
recognition of <a
href="https://en.wikipedia.org/wiki/Juneteenth">Juneteenth</a>, there
will be <strong>no class on Wednesday June 19th, 2024.</strong>.)</li>
<li><strong>Time:</strong> 1:30 p.m. - 4:50 p.m. ET</li>
</ul>
<p><br></p>
</div>
<div id="where" class="section level3">
<h3>Where</h3>
<ul>
<li><strong>Class Website:</strong> <a
href="http://jhudatascience.org/intro_to_r/"
class="uri">http://jhudatascience.org/intro_to_r/</a><br />
</li>
<li><strong>CoursePlus:</strong> <a
href="https://courseplus.jhu.edu/core/index.cfm/go/syl:syl.public.view/coid/21696/"
class="uri">https://courseplus.jhu.edu/core/index.cfm/go/syl:syl.public.view/coid/21696/</a></li>
<li>Course lectures and labs will be online through Zoom</li>
<li>Zoom link and Slack link will be emailed to students</li>
<li>Communication will mainly occur through Slack</li>
</ul>
<p><br></p>
</div>
<div id="instruction-team" class="section level3">
<h3>Instruction Team</h3>
<ul>
<li><strong>Instructors:</strong> <a
href="https://carriewright11.github.io/">Carrie Wright</a> (cwrigh60 at
jhu.edu), <a href="https://www.avahoffman.com/">Ava Hoffman</a>
(ava.hoffman at jhu.edu), <a href="https://clifmckee.github.io/">Clifton
McKee</a> (cmckee7 at jhu.edu)</li>
<li><strong>Teaching Assistants:</strong> Charlotte Clapham (cclapha1 at
jh.edu), Tashnim Rafa (trafa1 at jh.edu)</li>
</ul>
<p><br></p>
</div>
</div>
<div id="course-format" class="section level2">
<h2>Course Format</h2>
<ul>
<li><p>Each class will consist of 2 or 3 hour-long modules.</p></li>
<li><p>Each module features a lecture and an R programming lab, where
students apply the skills taught in the modules to real data in breakout
rooms.</p></li>
<li><p>Class sessions will be recorded and later posted.</p></li>
<li><p>If you have a question not covered during class, please post it
on Slack. This allows everyone to see it. If another student does not
answer your question (which we encourage!), we will try to answer it
within 24 hours. If you feel uncomfortable posting a question publicly,
let a TA or instructor know your question and we will post it for you
anonymously.</p></li>
<li><p>To get the most out of this class, if possible, we suggest
working virtually with a <strong>large monitor or two screens</strong>.
This setup allows you to follow along on Zoom while also doing the
hands-on coding.<br />
</p></li>
<li><details>
<summary>
<p><span style="color: #5383bb;"> <strong>Please click here for details
about using Zoom.</strong></span></p>
</summary>
<p>Zoom + Working Virtually</p>
<hr />
<ul>
<li>Please be aware that there is the option to use closed
captioning:</li>
</ul>
<div class="float">
<img src="docs/images/CC.png" alt="closed captioning on zoom" />
<div class="figcaption">closed captioning on zoom</div>
</div>
<ul>
<li>During lectures you can indicate how you feel about the pace of the
course like so:</li>
</ul>
<div class="float">
<img src="docs/images/slow_fast_reactions.png"
alt="reactions about pace" />
<div class="figcaption">reactions about pace</div>
</div>
<ul>
<li>In breakout room sessions you can ask for help like so:</li>
</ul>
<div class="float">
<img src="docs/images/help.png" alt="ask for help" />
<div class="figcaption">ask for help</div>
</div>
<ul>
<li>For directions on how to change breakout rooms click <a
href="https://docs.google.com/document/d/1YP1pZF1bIm66_Tl15Y3eHl8pGxNIASD33mKCtGCfQzc/edit?usp=sharing">here</a>.</li>
</ul>
<hr />
</details></li>
</ul>
<p><br></p>
</div>
<div id="course-evaluation" class="section level2">
<h2>Course Evaluation</h2>
<p>Course evaluations are very important for the school to determine
what courses to continue to support. It also helps us to improve the
course with your feedback.</p>
<ul>
<li>Use this link to access the evaluation: <a
href="https://courseevaluations.jhsph.edu"
class="uri">https://courseevaluations.jhsph.edu</a>.</li>
<li>Use your JHED ID or and password to log in. If you do not have a
JHED ID, sign in as a “Guest User” using the email provided to create
your JHU login during course registration. Please contact <a
href="mailto:JHSPH.courseeval@jhu.edu"
class="email">JHSPH.courseeval@jhu.edu</a> for assistance.<br />
</li>
<li>All non-auditing institute students (whether they are taking courses
for credit or not) are eligible to evaluate their courses.</li>
</ul>
<p><br></p>
</div>
<div id="assignments" class="section level2">
<h2>Assignments</h2>
<p><br></p>
<div id="grading" class="section level3">
<h3>Grading</h3>
<p>All assignments are due <strong>June 28th at 11:59pm ET</strong>.</p>
<table>
<thead>
<tr class="header">
<th align="left"><strong>Assignment</strong></th>
<th align="right"><strong>Percent of Grade</strong></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">Attendance/Participation</td>
<td align="right">20%</td>
</tr>
<tr class="even">
<td align="left">Homework 1</td>
<td align="right">15%</td>
</tr>
<tr class="odd">
<td align="left">Homework 2</td>
<td align="right">15%</td>
</tr>
<tr class="even">
<td align="left">Homework 3</td>
<td align="right">15%</td>
</tr>
<tr class="odd">
<td align="left">Final Project</td>
<td align="right">35%</td>
</tr>
<tr class="even">
<td align="left"><strong>Total</strong></td>
<td align="right">100%</td>
</tr>
</tbody>
</table>
<p><strong>Note</strong>: only people taking the course for credit must
turn in the assignments. However, we will evaluate all submitted
assignments in case others would like feedback on their work.</p>
<p><br></p>
</div>
<div id="homework" class="section level3">
<h3>Homework</h3>
<p>You should complete the following:</p>
<table>
<colgroup>
<col width="12%" />
<col width="22%" />
<col width="65%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"><strong>Module</strong></th>
<th align="center"><strong>Details</strong></th>
<th align="center"><strong>Code</strong></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">Homework 1</td>
<td align="center"><a href="docs/module_details/day0.html">Day 0
Instructions</a></td>
<td align="center"><a href="modules/HW/homework1.html">HTML</a></td>
</tr>
<tr class="even">
<td align="center">Homework 2</td>
<td align="center"></td>
<td align="center"><a href="modules/HW/homework2.Rmd">Rmd</a>, <a
href="modules/HW/homework2.html">HTML</a>, <a
href="modules/HW/homework2_Key.Rmd">Key</a>, <a
href="modules/HW/homework2_Key.html">Key HTML</a></td>
</tr>
<tr class="odd">
<td align="center">Homework 3</td>
<td align="center"></td>
<td align="center"><a href="modules/HW/homework3.Rmd">Rmd</a>, <a
href="modules/HW/homework3.html">HTML</a>, <a
href="modules/HW/homework3_Key.Rmd">Key</a>, <a
href="modules/HW/homework3_Key.html">Key HTML</a></td>
</tr>
</tbody>
</table>
<p><br></p>
</div>
<div id="final-project" class="section level3">
<h3>Final Project</h3>
<p>This project should entail:</p>
<ul>
<li>reading in a dataset of your choosing</li>
<li>doing some light data cleaning</li>
<li>performing some data summarization</li>
<li>creating a couple of visualizations</li>
<li>doing some very light statistical analysis, like regression or
t-tests</li>
</ul>
<p>You may use public datasets, or your own data for the project. If
using your own dataset, <strong>be sure any sensitive information is
protected</strong>.</p>
<p>Example projects can be found with the source code: <a
href="modules/Project_Example/Project_Example.Rmd">Rmd</a>, and the
output <a href="modules/Project_Example/Project_Example.html">html</a>
here.</p>
<p>See the <a
href="modules/Project_Guidelines/Project_Guidelines.html">guidelines/instructions</a>
for final projects, including dataset resources.</p>
<p><br></p>
</div>
<div id="submission" class="section level3">
<h3>Submission</h3>
<p>All assignments are due <strong>June 28th at 11:59pm ET</strong>.</p>
<p>Submit each assignment to the designated <a
href="https://courseplus.jhu.edu/core/index.cfm/go/db:main/coID/21696/">Drop
Box on CoursePlus</a>.</p>
<p><br></p>
</div>
<div id="assignment-extensions" class="section level3">
<h3>Assignment Extensions</h3>
<p>We know that you will try your best to submit assignments on time.
However, we understand that life happens. We can accept late assignments
with a deduction of 2% of your assignment score per day late.</p>
<p>For example, if you scored 9/10 on an assignment (90%) but turned it
in two days late, your score would be 8.6/10 (86%).</p>
<p><br></p>
</div>
</div>
<div id="code-of-conduct" class="section level2">
<h2>Code of Conduct</h2>
<p>We would like to create an open, safe, welcoming, diverse, inclusive,
intellectually stimulating, and hopefully fun class experience.</p>
<p>We strive to be a space in which individual differences are
respected, so that each individual can reach their fullest
potential.</p>
<p><br></p>
<div id="guidelines" class="section level3">
<h3>Guidelines</h3>
<ul>
<li>Demonstrating empathy and kindness toward other people<br />
</li>
<li>Giving and gracefully accepting constructive feedback<br />
</li>
<li>Avoiding making assumptions about others<br />
</li>
<li>Being respectful of differing opinions, viewpoints, and
experiences<br />
</li>
<li>Take the time to consider how your speech and actions may influence
others<br />
</li>
<li>Actively seek to acknowledge and respect the boundaries of other
members<br />
</li>
<li>Demonstrating academic integrity
<ul>
<li>Students can work together, but assignments must show unique
contributions from the student who turns in the assignment<br />
</li>
<li>Students can use online resources for help, but assignments must
show unique contributions from the student who turns in the assignment -
plagiarism is not allowed<br />
</li>
<li>If students are struggling, reach out to instructors or TAs as early
as possible</li>
</ul></li>
</ul>
<p>This applies to emails, surveys, Slack, Zoom, office hours, meetings
with other students, instructors, or TAs.</p>
<p><strong>Please reach out to a TA or instructor if you witness or
experience a violation of the class guidelines or other JHU codes of
conduct.</strong></p>
<p><br></p>
</div>
<div id="resources" class="section level3">
<h3>Resources</h3>
<ul>
<li><strong>JHU Student Code of Conduct:</strong> <a
href="https://studentaffairs.jhu.edu/policies-guidelines/student-code/"
class="uri">https://studentaffairs.jhu.edu/policies-guidelines/student-code/</a><br />
</li>
<li><strong>Hopkins School of Medicine:</strong> <a
href="https://www.hopkinsmedicine.org/research/resources/offices-policies/OPC/Research_Integrity/som_code_of_conduct_04302020.pdf"
class="uri">https://www.hopkinsmedicine.org/research/resources/offices-policies/OPC/Research_Integrity/som_code_of_conduct_04302020.pdf</a><br />
</li>
<li><strong>JHSPH Academic Ethics Code:</strong> <a
href="https://www.jhsph.edu/offices-and-services/student-affairs/resources/student-policies/_documents/academic-ethics-code.pdf"
class="uri">https://www.jhsph.edu/offices-and-services/student-affairs/resources/student-policies/_documents/academic-ethics-code.pdf</a></li>
</ul>
<p><strong>The University has developed avenues for reporting and for
seeking help including:</strong></p>
<ul>
<li>JHU Sexual Assault Helpline, 410-516-7333 (confidential)<br />
</li>
<li>Campus Safety and Security, 410-516-7777<br />
</li>
<li>University Sexual Assault Response and Prevention website<br />
</li>
<li>Johns Hopkins Compliance Hotline, 844-SPEAK2US (844-733-2528)<br />
</li>
<li>JHU Office of Institutional Equity 410-516-8075
(nonconfidential)<br />
</li>
<li>Johns Hopkins Student Assistance Program (JHSAP), 443-287-7000<br />
</li>
<li>University Health Services - Mental Health (UHS-MS),
410-955-1892<br />
</li>
<li>The Faculty and Staff Assistance Program (FASAP), 443-997-7000</li>
</ul>
</div>
</div>
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