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<div id="header">


<h1 class="title toc-ignore">STA305/1004 Fall 2019 Syllabus</h1>

</div>


<p><br></p>
<div id="instructor" class="section level1">
<h1>Instructor</h1>
<p>Professor Nathan Taback</p>
<p><a href="mailto:nathan.taback@utoronto.ca"
class="email">nathan.taback@utoronto.ca</a>
<i class="fas fa-paper-plane"></i></p>
<p>Office: SS6027C</p>
<p>Office hours: TBD</p>
</div>
<div id="class-time" class="section level1">
<h1>Class Time</h1>
<p>Teaching Assistants: TBD</p>
<p>Classroom sessions: T 14:00-16:00, R 10:00-11:00</p>
</div>
<div id="course-content" class="section level1">
<h1>Course Content</h1>
<p>This course will provide an introduction to the fundamental concepts
of the design of scientific studies including the design of experiments
and observational studies. Students will be become acquainted with
statistical methods used to design and analyze experiments and
observational studies. In particular, this course will cover:
experiments versus observational studies, clinical trial design,
comparing several groups using a completely randomized design,
randomized blocks, Latin squares, incomplete block designs, factorial
designs, causal inference in randomized and non-randomized studies, and
adjusting for selection bias using propensity score methods.</p>
<p>The learning objectives of this course are:</p>
<ul>
<li>Understand the ideas, principles, and considerations that are common
to the design and analysis of scientific studies including the
statistical design of experiments and observational studies.</li>
<li>Develop a statistical toolbox of methods for the design and analysis
of experiments and observational studies.</li>
<li>Identify appropriate uses and interpretations of experimental
designs, and observational studies, including their strengths and
limitations.</li>
</ul>
<div id="topics" class="section level2">
<h2>Topics</h2>
<div id="experiments-observational-studies-and-causal-inference"
class="section level3">
<h3>Experiments, observational studies, and causal inference</h3>
<p>Experiments versus observational studies, and causal inference in
randomized experiments.</p>
</div>
<div id="selection-bias-in-observational-studies"
class="section level3">
<h3>Selection Bias in Observational Studies</h3>
<p>Causal inference in randomized experiments versus observational
studies. Introduction to the propensity score and three ways to use the
propensity score to adjust for selection bias: matching; sub
classification; direct regression adjustment.</p>
</div>
<div id="probability-and-statistics" class="section level3">
<h3>Probability and Statistics</h3>
<p>Mathematical statistics used in experimental design.</p>
</div>
<div id="comparing-several-groups" class="section level3">
<h3>Comparing Several Groups</h3>
<p>Comparing several groups in an experimental and observational setting
and deciding whether differences that are found are likely to be real or
due to chance.</p>
</div>
<div id="power-and-sample-size" class="section level3">
<h3>Power and Sample Size</h3>
<p>Power and sample size will be introduced for several designs.
Applications will include the design and analysis of clinical trials
with continuous or binary endpoints.</p>
</div>
<div id="blocking-techniques" class="section level3">
<h3>Blocking Techniques</h3>
<p>Blocked designs, Latin squares, randomized incomplete block
designs.</p>
</div>
<div id="factorial-designs" class="section level3">
<h3>Factorial Designs</h3>
<p>Factorial, blocked factorial, and fractional factorial designs will
be discussed.</p>
</div>
<div id="split-plot-designs" class="section level3">
<h3>Split Plot Designs</h3>
<p>Split plot designs will be discussed as an example of restricted
randomization in the design of experiments.</p>
</div>
</div>
</div>
<div id="course-books" class="section level1">
<h1>Course Books</h1>
<div id="required" class="section level2">
<h2>Required</h2>
<p><a href = "https://scidesign.github.io/designbook/" target="_blank">
Taback, N. (2019). Design of Experiments and Observational Studies.
</a></p>
</div>
<div id="optional" class="section level2">
<h2>Optional</h2>
<ol style="list-style-type: decimal">
<li><p>Statistics for Experimenters: Design, Innovation, and Discovery.
Box, G.E.P., Hunter, J.S., Hunter, W.G. Wiley 2nd Ed. 2005</p></li>
<li><p>Design and Analysis of Experiments. Dean, A., and Voss, D.
Springer. 1999. UofT link to electronic copy: <a
href="http://go.utlib.ca/cat/2573215"
class="uri">http://go.utlib.ca/cat/2573215</a></p></li>
<li><p>Design of Observational Studies. Rosenbaum, P. R. Springer 2010.
UofT link to electronic copy: <a href="http://go.utlib.ca/cat/7890274"
class="uri">http://go.utlib.ca/cat/7890274</a></p></li>
<li><p>Experiments: planning, analysis, and optimization. Wu, C.F.J.,
Hamada, M.S. Wiley, 2009, 2nd ed.</p></li>
<li><p>Causal inference for statistics, social, and biomedical sciences.
Imbens and Rubin. Cambridge University Press, 2015. <a
href="http://go.utlib.ca/cat/10127748"
class="uri">http://go.utlib.ca/cat/10127748</a></p></li>
</ol>
<p>NB: Textbooks 2,3, 5 are available electronically through the UofT
library (i.e., electronic copies of both these textbooks are available
at no extra cost)</p>
</div>
</div>
<div id="course-materials-including-lecture-notes"
class="section level1">
<h1>Course Materials, including lecture notes</h1>
<p>Course materials are provided for the exclusive use of enrolled
students. Do not share them with others. I do not want to discover that
a student has put any of my materials into the public domain, has sold
my materials, or has given my materials to a person or company that is
using them to earn money. The University will support me in asserting
and pursuing my rights, and my copyrights, in such matters.</p>
</div>
<div id="evaluation" class="section level1">
<h1>Evaluation</h1>
<p>Students will be evaluated according to the <a
href="http://www.governingcouncil.utoronto.ca/Assets/Governing+Council+Digital+Assets/Policies/PDF/grading.pdf">University
Assessment and Grading Practices Policy</a>.</p>
<p>Undergraduate students will be evaluated according to the following
marking scheme.</p>
<table>
<thead>
<tr class="header">
<th></th>
<th>Weight</th>
<th>Date</th>
<th>Time</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>Term Test #1</td>
<td>20%</td>
<td>Oct. 8</td>
<td>14:00</td>
</tr>
<tr class="even">
<td>Term Test #2</td>
<td>20%</td>
<td>Nov. 19</td>
<td>14:00</td>
</tr>
<tr class="odd">
<td>Draft/proposal project</td>
<td>5%</td>
<td>TBD</td>
<td>TBD</td>
</tr>
<tr class="even">
<td>Final project</td>
<td>10%</td>
<td>Dec. 5</td>
<td>23:59</td>
</tr>
<tr class="odd">
<td>Final Exam</td>
<td>45%</td>
<td>Scheduled by Faculty</td>
<td></td>
</tr>
</tbody>
</table>
<p>The tests will be written during class time (14:10 – 15:40) in a
location to be announced.</p>
<p>You are allowed a two-sided 8-1/2”x 11” (standard letter size)
hand-written aid sheet on the term test and a two-sided hand-written aid
sheet on the final exam. You must bring your student identification to
the term tests and the final exam.</p>
<p>You will not need to know R syntax on the tests and exam, but you
will need to know how to interpret output from R.</p>
</div>
<div id="class-schedule" class="section level1">
<h1>Class Schedule</h1>
<p>A tentative class schedule can be found <a
href="schedule_fall2019.html">here</a>.</p>
<div id="marking-concerns" class="section level2">
<h2>Marking concerns</h2>
<p>Any requests to have marked work re-evaluated must be made in writing
to the instructor within one week of the date the work was returned. The
request must contain a justification for consideration.</p>
</div>
<div id="missed-tests" class="section level2">
<h2>Missed Tests</h2>
<ul>
<li><p>If a test is missed for a valid reason, you must submit
documentation to the course instructor.</p></li>
<li><p>If a test is missed for a valid medical reason, you must submit
the <a
href="http://www.illnessverification.utoronto.ca/index.php">University
of Toronto Verification of Student Illness or Injury form</a> to your
instructor within one week of the test.</p></li>
<li><p>The form will only be accepted as valid if the form is filled out
according to the instructions on the form.</p></li>
<li><p>The form must indicate that the degree of incapacitation on
academic functioning is moderate, serious, or severe in order to be
considered a valid medical reason for missing the term test. If the form
indicates that the degree of incapacitation on academic functioning is
negligible or mild then this will NOT be considered a valid medical
reason.</p></li>
<li><p>If a test is missed for a valid reason then half the weight of
the test will be shifted to the other midterm and half will be shifted
to the final exam. In this case the other term test will be worth 30%
and the final exam will be worth 55%.</p></li>
<li><p>If a student misses <strong>BOTH</strong> term tests for any
reason then an <a href="https://en.wikipedia.org/wiki/Oral_exam">oral
exam</a> with members of the teaching team will be scheduled at a
mutually convenient time in lieu of the two term tests worth
40%.</p></li>
<li><p>Students must complete at least one midterm test or oral exam. If
a student misses both midterm tests and does not take an oral exam
before the end of term then a grade of zero will be assigned to the term
work.</p></li>
<li><p>Other reasons for missing a test will require prior approval by
your instructor. If prior approval is not received for a non-medical
reason, then you will receive a term test grade of zero.</p></li>
</ul>
</div>
<div id="late-project-submission" class="section level2">
<h2>Late Project Submission</h2>
<p>If the draft/propsal project or final project is submitted after the
due date then a late penalty of 20% per day (i.e., 24 hours) will be
applied to the part of the project handed in late. For example, if the
draft/proposal project is submitted after 5 days (including weekend
days) then you will receive a grade of zero for the draft/proposal.</p>
</div>
</div>
<div id="computing" class="section level1">
<h1>Computing</h1>
<p>We will use R for all examples. R is freely available for download at
<a href="http://cran.r-project.org"
class="uri">http://cran.r-project.org</a> for Windows, Mac, and Linux
operating systems. For the tests and exam, you will need to know how to
interpret output from R.</p>
<div id="jupyter-notebook" class="section level2">
<h2>Jupyter Notebook</h2>
<blockquote>
<p>The Jupyter Notebook is an open-source web application that allows
you to create and share documents that contain live code, equations,
visualizations and narrative text. (Ref: <a href="https://jupyter.org"
class="uri">https://jupyter.org</a>)</p>
</blockquote>
<p>R can be run in a Jupyter notebook in any web brwoser by logging into
<a href="https://utoronto.syzygy.ca"
class="uri">https://utoronto.syzygy.ca</a> with your UTORid.</p>
<p>To get started using R in a Jupyter notebook see this <a
href="jupyterstarter.html">page</a></p>
</div>
<div id="rstudio" class="section level2">
<h2>RStudio</h2>
<p>RStudio is a fantastic integrated development environment (IDE) for
R. It is freely available at <a
href="https://www.rstudio.com/products/rstudio/"
class="uri">https://www.rstudio.com/products/rstudio/</a></p>
<p>I am assuming that students have never used R before. I will provide
you with the R syntax for all examples in lecture, which should be
sufficient for you to complete the practice problems.</p>
</div>
</div>
<div id="calculators" class="section level1">
<h1>Calculators</h1>
<p>You will need a calculator. Any calculator that has logarithmic
functions will be sufficient. Calculators on phones or other devices
equipped to communicate with the outside world (for example, through the
internet or cellular or satellite phone networks) will not be permitted
during the term tests or final exam.</p>
</div>
<div id="getting-help" class="section level1">
<h1>Getting Help</h1>
</div>
<div id="online-discussion-board" class="section level1">
<h1>Online Discussion Board</h1>
<p>This term you will have the option to use Piazza for class
discussion. If you decide not to use Piazza it will not disadvantage you
in any way, and will not affect official University outcomes (e.g.,
grades and learning opportunities). If you choose not to opt-into Piazza
then you can ask questions or discuss course material with the
instructor or TAs during office hours.</p>
<p>Be sure to read <a href="https://piazza.com/legal/privacy">Piazza’s
Privacy Policy</a> and <a href="https://piazza.com/legal/terms">Terms of
Use</a> carefully. Take time to understand and be comfortable with what
they say. They provide for substantial sharing and disclosure of your
personal information held by Piazza, which affects your privacy. If you
decide to participate in Piazza, only provide content that you are
comfortable sharing under the terms of the Privacy Policy and Terms of
Use.</p>
<p>The Piazza system is highly catered to getting you help fast and
efficiently from classmates, the TA, and the lecturers. Rather than
emailing questions to the teaching staff, we encourage you to post your
questions on Piazza. To sign up for the discussion forum click on the
link :</p>
<p><a href="https://piazza.com/utoronto.ca/fall2019/sta305h1004/home"
class="uri">https://piazza.com/utoronto.ca/fall2019/sta305h1004/home</a></p>
<div id="additional-help" class="section level2">
<h2>Additional help</h2>
<p>Need extra help with the coursework? Here are some options: - For
continued class discussion and questions outside of class, try posting
on the discussion forums. The instructor and TAs will be monitoring them
regularly. - You can visit your instructor or the teaching assistants
during their office hours.</p>
<p>E-mail should only be used for emergencies or personal matters.</p>
</div>
</div>
<div id="how-to-communicate-with-your-instructor"
class="section level1">
<h1>How to communicate with your instructor</h1>
<p>Questions about course material such as:</p>
<ul>
<li><p>How do I do question 3.7 in the textbook?</p></li>
<li><p>What is standard deviation?</p></li>
<li><p>When is the midterm?</p></li>
</ul>
<p>Can be posted on the discussion forums. Questions can be posted
anonymously (so that the author is anonymous to other students but not
to the instructors), if desired.</p>
<p>For private communication, such as: I missed the test because I was
ill e-mail your instructor.</p>
<p>Use your utoronto.ca e-mail account to ensure that your message
doesn’t automatically go to a Junk folder and include your full name and
student number.</p>
</div>
<div id="religious-accommodation" class="section level1">
<h1>Religious Accommodation</h1>
<p>As a student at the University of Toronto, you are part of a diverse
community that welcomes and includes students and faculty from a wide
range of cultural and religious traditions. For my part, I will make
every reasonable effort to avoid scheduling tests, examinations, or
other compulsory activities on religious holy days not captured by
statutory holidays. Further to University Policy, if you anticipate
being absent from class or missing a major course activity (such as a
test or in-class assignment) due to a religious observance, please let
me know as early in the course as possible, and with sufficient notice
(at least two to three weeks), so that we can work together to make
alternate arrangements.</p>
</div>
<div id="students-with-disabilities-or-accommodation-requirements"
class="section level1">
<h1>Students with Disabilities or Accommodation Requirements</h1>
<p>Students with diverse learning styles and needs are welcome in this
course. If you have an acute or ongoing disability issue or
accommodation need, you should register with Accessibility Services (AS)
at the beginning of the academic year by visiting <a
href="http://www.studentlife.utoronto.ca/as/new-registration"
class="uri">http://www.studentlife.utoronto.ca/as/new-registration</a>.
Without registration, you will not be able to verify your situation with
your instructors, and instructors will not be advised about your
accommodation needs. AS will assess your situation, develop an
accommodation plan with you, and support you in requesting accommodation
for your course work. Remember that the process of accommodation is
private: AS will not share details of your needs or condition with any
instructor, and your instructors will not reveal that you are registered
with AS.</p>
</div>
<div id="academic-integrity" class="section level1">
<h1>Academic Integrity</h1>
<p>All students, faculty and staff are expected to follow the
University’s guidelines and policies on academic integrity. For
students, this means following the standards of academic honesty when
writing assignments, collaborating with fellow students, and writing
tests and exams. Ensure that the work you submit for grading represents
your own honest efforts. Plagiarism—representing someone else’s work as
your own or submitting work that you have previously submitted for marks
in another class or program—is a serious offence that can result in
sanctions. Speak to me or your TA for advice on anything that you find
unclear. To learn more about how to cite and use source material
appropriately and for other writing support, see the U of T writing
support website at <a href="http://www.writing.utoronto.ca"
class="uri">http://www.writing.utoronto.ca</a>. Consult the Code of
Behaviour on Academic Matters for a complete outline of the University’s
policy and expectations. For more information, please see <a
href="https://www.artsci.utoronto.ca/current/academic-advising-and-support/student-academic-integrity"
class="uri">https://www.artsci.utoronto.ca/current/academic-advising-and-support/student-academic-integrity</a>
and <a href="http://academicintegrity.utoronto.ca"
class="uri">http://academicintegrity.utoronto.ca</a></p>
</div>
<div id="specific-medical-circumstances" class="section level1">
<h1>Specific Medical Circumstances</h1>
<p>If you become ill and it affects your ability to do your academic
work, consult me right away. Normally, I will ask you for medical
documentation in support of your specific medical circumstances. The
University’s Verification of Student Illness or Injury (VOI) form is
recommended because it indicates the impact and severity of the illness,
while protecting your privacy about the details of the nature of the
illness. You can submit a different form (like a letter from a doctor),
as long as it is an original document, and it contains the same
information as the VOI. For more information, please see <a
href="http://www.illnessverification.utoronto.ca"
class="uri">http://www.illnessverification.utoronto.ca</a> If you get a
concussion, break your hand, or suffer some other acute injury, you
should register with Accessibility Services as soon as possible.</p>
</div>
<div id="accommodation-for-personal-reasons" class="section level1">
<h1>Accommodation for Personal Reasons</h1>
<p>There may be times when you are unable to complete course work on
time due to non-medical reasons. If you have concerns, speak to me or to
an advisor in your College Registrar’s office; they can help you to
decide if you want to request an extension or accommodation. They may be
able to provide you with a College Registrar’s letter of support to give
to your instructors, and importantly, connect you with other resources
on campus for help with your situation.</p>
</div>
<div id="your-responsibilities" class="section level1">
<h1>Your responsibilities</h1>
<p>The classroom sessions for this class are designed to actively engage
you in the course material. We hope you’ll find them interesting,
challenging, and fun, and an excellent opportunity to truly learn the
material.</p>
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<br> <br>

<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.


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