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\begin_layout Title
STAT 243: Introduction to Statistical Computing
\begin_inset Newline newline
\end_inset
Fall 2020 (Paciorek)
\end_layout
\begin_layout Subsection*
Course Description
\end_layout
\begin_layout Standard
Statistics 243 is an introduction to statistical computing, taught using
R.
The course will cover both programming concepts and statistical computing
concepts.
Programming concepts will include data and text manipulation, data structures,
functions and variable scope, regular expressions, debugging, and parallel
processing.
Statistical computing topics will include working with large datasets,
numerical linear algebra, computer arithmetic/precision, simulation studies
and Monte Carlo methods, numerical optimization, and numerical integration/diff
erentiation.
A goal is that coverage of these topics complement the models/methods discussed
in the rest of the statistics/biostatistics graduate curriculum.
We will also cover the basics of UNIX/Linux, in particular some basic shell
scripting and operating on remote servers, as well as a bit of Python.
\end_layout
\begin_layout Standard
While the course is taught using R and you will learn a lot about using
R at an advanced level, the focus of the course is statistical computing
more generally.
Also, this is not a course that will cover specific statistical/data analysis
methods.
\end_layout
\begin_layout Standard
Informal prerequisites: If you are not a statistics or biostatistics graduate
student, please chat with me if you're not sure if this course makes sense
for you.
A background in calculus, linear algebra, probability and statistics is
expected, as well as a basic ability to operate on a computer (but I do
not assume familiarity with the UNIX-style command line/terminal/shell).
Furthermore, I'm expecting you will know the basics of R, at the level
of the Modules 1-5 in the R bootcamp offered Aug.
10-13, 2020.
If you don't have that background you'll need to spend time in the initial
couple weeks getting up to speed.
All the material from the bootcamp is
\begin_inset CommandInset href
LatexCommand href
name "available here"
target "https://github.com/berkeley-scf/r-bootcamp-fall-2020/archive/master.zip"
literal "false"
\end_inset
(plus I can give you access to the bootcamp videos), we'll have a hands-on
practice session in Lab 0 on Friday August 28, and the GSI can also provide
assistance.
\end_layout
\begin_layout Standard
\series bold
DISCLAIMER: Given the evolving situation, we may need to adjust some of
the approaches and policies stated here, but I will try to be very clear
if/when I do this.
\end_layout
\begin_layout Subsection*
Objectives of the course
\end_layout
\begin_layout Standard
The goals of the course are that, by the end of the course, students be
able to:
\end_layout
\begin_layout Itemize
operate effectively in a UNIX environment and on remote servers;
\end_layout
\begin_layout Itemize
program effectively in R with an advanced knowledge of R functionality and
an understanding of general programming concepts and principles;
\end_layout
\begin_layout Itemize
be familiar with concepts and tools for reproducible research and good scientifi
c computing practices; and
\end_layout
\begin_layout Itemize
understand in depth and be able to make use of principles of numerical linear
algebra, optimization, and simulation for statistics- and data science-related
analyses and research.
\end_layout
\begin_layout Subsection*
Personnel
\end_layout
\begin_layout Itemize
Instructor:
\begin_inset Separator latexpar
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Chris Paciorek ([email protected])
\end_layout
\end_deeper
\begin_layout Itemize
GSI
\begin_inset Separator latexpar
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Zoe Vernon ([email protected])
\end_layout
\end_deeper
\begin_layout Itemize
We'll post office hours on the Github site README.
I expect we'll have some hours where you can just show up and others where
we have sign-up slots for individual-specific questions.
\end_layout
\begin_layout Itemize
\series bold
When to see us about an assignment
\series default
: We're here to help, including providing guidance on assignments.
You don't want to be futilely spinning your wheels for a long time getting
nowhere.
That said, before coming to see us about a difficulty, you should try something
a few different ways and define/summarize what is going wrong or where
you are getting stuck.
\end_layout
\begin_layout Subsection*
Class sessions
\end_layout
\begin_layout Standard
Given the virtual context, class sessions will be somewhat different than
the usual university course.
\end_layout
\begin_layout Standard
Each unit has a set of notes and demo code that will form the basis of the
instruction for that unit.
For some material, we will make use of tutorials provided by the SCF (see
link below).
\end_layout
\begin_layout Itemize
I will assign reading and pre-recorded videos for each unit.
There will be a short assignment that will check your understanding of
the materials.
\end_layout
\begin_layout Itemize
Some (but not all) class sessions will be live on Zoom, focused on presentation
of topics benefiting from the live format, group work on problems, and
discussion.
All of the main sessions (but not breakout groups) will be recorded for
anyone in the class (but not anyone else) to view later.
In some class sessions you will be asked to work on a group problem and
will need to turn in your answers.
\end_layout
\begin_layout Itemize
Those not able to attend live class sessions will have the option of watching
the video separately but will still need to turn in work related to the
class session.
\end_layout
\begin_layout Standard
My goal is to have the class sessions that we do hold live be an interactive
environment.
Part of this will involve group work where I will pose questions to the
class to think about, respond to via Google forms, and discuss.
During times where I am doing a demo or otherwise presenting, I encourage
you to ask questions verbally and (likely) through the Piazza forum.
\end_layout
\begin_layout Standard
\end_layout
\begin_layout Subsubsection*
Zoom guidance
\end_layout
\begin_layout Itemize
Microphones and questions: please keep your microphone muted, but feel free
to interrupt me with a question or raise your virtual hand.
I'll also try to remember to pause for questions regularly.
\end_layout
\begin_layout Itemize
We'll experiment with having text-based questions in Piazza during class
sessions.
Please post to the 'class' folder on Piazza.
\end_layout
\begin_layout Itemize
If possible please have your video on during class sessions.
Unless absolutely necessary not to, please have your video on when working
in a group or asking me a question.
\end_layout
\begin_layout Itemize
Please do your best to stay focused during class time and section group
work (I know this can be hard).
\end_layout
\begin_deeper
\begin_layout Itemize
I ask that you leave your phone elsewhere and keep other windows/apps on
your computer closed or out of your direct view.
\end_layout
\end_deeper
\begin_layout Itemize
If you have concerns about being recorded in the Zoom sessions, please let
me know so we can discuss how you can avoid being recorded.
\end_layout
\begin_layout Itemize
If you have trouble accessing a Zoom session or don't see me there, please
check Piazza for updates.
\end_layout
\begin_layout Standard
Student backgrounds with computing will vary.
For those of you with limited background on a topic, I encourage you to
ask questions on Piazza and during class.
For those of you with extensive background on a topic (there will invariably
be some topics where one of you will know more about it than I do), I encourage
you to pitch in with your perspective.
In general, there are many ways to do things on a computer, particularly
in a UNIX environment and in R, so it will help everyone (including me)
if we hear multiple perspectives/ideas.
\end_layout
\begin_layout Subsection*
Course websites: Github, Piazza, GradeScope, and bCourses
\end_layout
\begin_layout Standard
Key websites for the course are:
\end_layout
\begin_layout Itemize
Github for course content:
\begin_inset CommandInset href
LatexCommand href
target "https://github.com/berkeley-stat243/stat243-fall-2020"
literal "false"
\end_inset
, including logistics info on the main Github page (scroll down below the
files listing).
\end_layout
\begin_layout Itemize
SCF tutorials for additional content:
\begin_inset CommandInset href
LatexCommand href
target "https://statistics.berkeley.edu/computing/training/tutorials"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
Piazza site for discussions/Q&A (also linked from bCourses):
\begin_inset CommandInset href
LatexCommand href
target "https://piazza.com/berkeley/fall2020/stat243"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
bCourses site for course recordings, Zoom links, and possibly some other
materials:
\end_layout
\begin_deeper
\begin_layout Standard
\begin_inset CommandInset href
LatexCommand href
name "https://bcourses.berkeley.edu/courses/1497598"
target "https://bcourses.berkeley.edu/courses/1497598"
literal "false"
\end_inset
.
\end_layout
\end_deeper
\begin_layout Itemize
Gradescope for assignments (also linked from bCourses):
\begin_inset CommandInset href
LatexCommand href
target "https://www.gradescope.com/courses/166974"
literal "false"
\end_inset
\end_layout
\begin_layout Standard
All course materials will be posted on Github except for pre-recorded videos
and class Zoom recordings, which will be in bCourses.
\end_layout
\begin_layout Standard
We will use the course Piazza site for communication (announcements, questions,
and discussion).
You should ask questions about class material and problem sets through
Piazza.
Please use this site for your questions so that either Zoe or I can respond
and so that everyone can benefit from the discussion.
I suggest you to modify your settings on Piazza so you are informed by
email of postings.
I strongly encourage you to respond to or comment on each other's questions
as well (this will help your class participation grade), although of course
you should not provide a solution to a problem set problem.
If you have a specific administrative question you need to direct just
to me, it's fine to email me directly.
But if you simply want to privately ask a question about content, then
just come to an office hour or see me after class.
\end_layout
\begin_layout Standard
In addition, we will use Gradescope for viewing grades.
\end_layout
\begin_layout Standard
\begin_inset Note Note
status open
\begin_layout Plain Layout
I will set up a course Wiki on Github, building off the Wiki from 2015.
The goal is to build up a useful set of webpages that provide tips on statistic
al computing and programming.
So if you figure out a clever way to do something, find a useful R function
or package, have a way to clean up the Wiki, or see a useful reference
to link to, please contribute this to the Wiki.
One way to get credit for class participation is to contribute to the Wiki.
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Note Note
status open
\begin_layout Plain Layout
We will make use of the discussion board on the website for answering questions.
Unless the issue is of a personal nature, please post questions to the
board rather than by email to me or the GSI.
Therefore, please check the site regularly.
I will also make announcements and provide material through the website,
with announcements also going out as email, so please check your email
regularly.
\end_layout
\begin_layout Plain Layout
Please don't email the bSpace page; just use the email addresses above for
the instructor or GSI.
\end_layout
\end_inset
\end_layout
\begin_layout Subsection*
Course material
\end_layout
\begin_layout Itemize
Primary materials: Course notes on Github and video recordings on bCourses.
\end_layout
\begin_layout Itemize
Back-up textbooks:
\end_layout
\begin_deeper
\begin_layout Itemize
For bash: Newham, Cameron and Rosenblatt, Bill.
Learning the bash Shell (available electronically through OskiCat:
\begin_inset CommandInset href
LatexCommand href
target "http://uclibs.org/PID/77225"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
For R:
\begin_inset Separator latexpar
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Adler, Joseph; R in a Nutshell (available electronically through OskiCat:
\begin_inset CommandInset href
LatexCommand href
target "http://uclibs.org/PID/151634"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
Wickham, Hadley: Advanced R:
\begin_inset CommandInset href
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name "http://adv-r.had.co.nz/"
target "http://adv-r.had.co.nz/"
literal "false"
\end_inset
\end_layout
\end_deeper
\begin_layout Itemize
For statistical computing topics:
\end_layout
\begin_deeper
\begin_layout Itemize
Gentle, James.
Computational Statistics (available electronically through OskiCat:
\begin_inset CommandInset href
LatexCommand href
target "http://dx.doi.org/10.1007/978-0-387-98144-4"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
Gentle, James.
Matrix Algebra
\begin_inset CommandInset href
LatexCommand href
target "https://link-springer-com.libproxy.berkeley.edu/book/10.1007%2F978-3-319-64867-5"
literal "false"
\end_inset
or Numerical Linear Algebra with Applications in Statistics
\begin_inset CommandInset href
LatexCommand href
target "https://link-springer-com.libproxy.berkeley.edu/chapter/10.1007/978-1-4612-0623-1_1"
literal "false"
\end_inset
\end_layout
\end_deeper
\begin_layout Itemize
Other resources with more details on particular aspects of R:
\end_layout
\begin_deeper
\begin_layout Itemize
Chambers, John; Software for Data Analysis: Programming with R (available
electronically through OskiCat:
\begin_inset CommandInset href
LatexCommand href
target "http://dx.doi.org/10.1007/978-0-387-75936-4"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
Xie, Yihui; Dynamic documents with R and knitr.
(available
\begin_inset CommandInset href
LatexCommand href
name "electronically through Oskicat"
target "http://oskicat.berkeley.edu/search~S1?/tDynamic+documents+with+R+and+knitr/tdynamic+documents+with+r+and+knitr/1%2C1%2C4%2CB/frameset&FF=tdynamic+documents+with+r+and+knitr&3%2C%2C4"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
Nolan, Deborah and Temple Lang, Duncan.
XML and Web Technologies for Data Sciences with R.
\begin_inset CommandInset href
LatexCommand href
target "https://link.springer.com/book/10.1007%2F978-1-4614-7900-0"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
The R-intro and R-lang documentation.
\begin_inset CommandInset href
LatexCommand href
target "https://www.cran.r-project.org/manuals.html"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
Murrell, Paul; R Graphics, 2nd ed.
\begin_inset CommandInset href
LatexCommand href
target "http://www.stat.auckland.ac.nz/~paul/RG2e/"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
Murrell, Paul; Introduction to Data Technologies.
\begin_inset CommandInset href
LatexCommand href
target "http://www.stat.auckland.ac.nz/~paul/ItDT/"
literal "false"
\end_inset
\end_layout
\end_deeper
\begin_layout Itemize
Other resources with more detail on particular aspects of statistical computing
concepts:
\end_layout
\begin_deeper
\begin_layout Itemize
Lange, Kenneth; Numerical Analysis for Statisticians, 2nd ed.
(first edition is available electronically through OskiCat:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\begin_inset CommandInset href
LatexCommand href
target "https://link.springer.com/book/10.1007%2Fb98850"
literal "false"
\end_inset
)
\end_layout
\begin_layout Itemize
Monahan, John; Numerical Methods of Statistics (available electronically
through OskiCat:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\begin_inset CommandInset href
LatexCommand href
target "http://dx.doi.org/10.1017/CBO9780511977176"
literal "false"
\end_inset
)
\end_layout
\end_deeper
\end_deeper
\begin_layout Standard
\begin_inset Note Note
status open
\begin_layout Plain Layout
Lange - Optimization
\end_layout
\end_inset
\end_layout
\begin_layout Subsection*
Section
\end_layout
\begin_layout Standard
The GSI will lead section each week.
Given the virtual format, our plan is to have each student sign up for
a half-hour within the Friday 12-4 pm time window, with those in incompatible
time zones accommodated separately.
Discussion sections will generally involve group work on various topics
(version control, debugging, testing, Python, etc.), discussion of problem
set solutions, or discussion of a particular topic.
Generally, the GSI will provide some written or pre-recorded video material
to get you started, rather than doing live presentation.
She will then circulate amongst the groups in Zoom breakout rooms.
\end_layout
\begin_layout Standard
If at all possible, please have your cameras on during group work in section
and when interacting with the GSI.
\end_layout
\begin_layout Standard
For those unable to make section (primarily a few of you in Asia), we will
likely have a combined section/office hour time late in the day Wednesday
(Pacific time) / early Thursday (Asia times).
\end_layout
\begin_layout Subsection*
Computing Resources
\end_layout
\begin_layout Standard
Most work for the course can be done on your laptop.
Later in the course we'll also use the Statistics department cluster.
You can also use the campus Datahub to access a bash shell or run RStudio.
\end_layout
\begin_layout Standard
The software needed for the course is as follows:
\end_layout
\begin_layout Itemize
Access to the UNIX command line (bash shell)
\end_layout
\begin_layout Itemize
Git
\end_layout
\begin_layout Itemize
R (RStudio is recommended but by no means required)
\end_layout
\begin_layout Itemize
Python (later in the course)
\end_layout
\begin_layout Standard
Some tips for software installation (and access to Datahub) are in the 'howtos'
directory of the Git repository.
In particular, please see 'accessingUnixCommandLine.html' for options of
how to access a bash shell.
\end_layout
\begin_layout Subsection*
Course requirements and grading
\end_layout
\begin_layout Subsubsection*
Course grades
\end_layout
\begin_layout Standard
The grade for this course is primarily based on assignments due every 1-2
weeks, a short exam in November (or possibly two quizzes - one in early
October and one in mid-November), and a final group project.
I will also provide extra credit questions on some problem sets.
There is no final exam.
50% of the grade is based on the problem sets, 25% on the exam, 15% on
the project, and 10% on your class participation (primarily the reading/video
assignments and responses to the in-class Google forms questions, as well
as participation in the Piazza discussions).
\end_layout
\begin_layout Standard
Grades will generally be As and Bs.
An A involves doing all the work, getting full credit on most of the problem
sets, showing competence on the exam, and doing a thorough job on the final
project.
\end_layout
\begin_layout Subsubsection*
Problem sets
\end_layout
\begin_layout Standard
We will be less willing to help you if you come to our office hours or post
a question online at the last minute.
Working with computers can be unpredictable, so give yourself plenty of
time for the assignments.
\end_layout
\begin_layout Standard
There are several rules for submitting your assignments.
\end_layout
\begin_layout Enumerate
You should prepare your assignments using either \SpecialChar LaTeX
plus knitr or R Markdown.
(If you're a Statistics student, I encourage you use \SpecialChar LaTeX
plus knitr).
\end_layout
\begin_layout Enumerate
Problem set submission consists of
\series bold
both
\series default
of the following:
\begin_inset Separator latexpar
\end_inset
\end_layout
\begin_deeper
\begin_layout Enumerate
A PDF submitted electronically through Gradescope, generally (but not always)
\series bold
by the start of class (10 am)
\series default
on the due date, and
\end_layout
\begin_layout Enumerate
An electronic copy of the PDF, code file, and R Markdown/knitr document
pushed to your class Github repository, following the instructions to be
provided by the GSI.
\end_layout
\begin_layout Standard
\series bold
On-time submission will be determined based on the time stamp of when the
PDF is submitted to gradeScope.
\end_layout
\end_deeper
\begin_layout Enumerate
Answers should consist of textual response or mathematical expressions as
appropriate, with key chunks of code embedded within the document.
Extensive additional code can be provided as an appendix.
Before diving into the code for a problem, you should say what the goal
of the code is and your strategy for solving the problem.
\series bold
Raw code without explanation is not an appropriate solution.
\end_layout
\begin_layout Enumerate
Any mathematical derivations may be done by hand and scanned with your phone
if you prefer that to writing up \SpecialChar LaTeX
equations.
\end_layout
\begin_layout Standard
Note: knitr is a tool that allows one to embed chunks of code within \SpecialChar LaTeX
documents.
It can also be used with the \SpecialChar LyX
GUI front-end to \SpecialChar LaTeX
.
R Markdown is an extension to the Markdown markup language that allows
one to embed R code within an HTML document.
Please see the dynamics document tutorial on the SCF tutorials website;
there will be additional information in the first section and on the first
problem set.
\end_layout
\begin_layout Standard
\begin_inset Note Note
status open
\begin_layout Plain Layout
I'm also open to you defining your own assignment for a given topic, if
you are working on a specific problem.
E.g., instead of working on a particular text manipulation problem I assign,
you might work with your own text data.
Check with me before forging ahead.
\end_layout
\end_inset
\end_layout
\begin_layout Subsubsection*
Problem set grading
\end_layout
\begin_layout Standard
The grading scheme for problem sets is as follows.
Each problem set will receive a numeric score for (1) presentation and
explanation of results, (2) technical accuracy of code or mathematical
derivation, and (3) code quality/style and creativity.
For each of these three components, the possible scores are:
\end_layout
\begin_layout Itemize
0 = no credit,
\end_layout
\begin_layout Itemize
1 = partial credit (you did some of the problems but not all),