Description and Outline
Statistics 159 is a course designed to cover philosophy, software tools,
principles and best practices for reproducible computational research.
Time permitting, the topics covered during the course include
(not necessarily in this order):
Shell (Bash) & Command Line Interface (CLI)
Version Control with Git
Project Hosting with GitHub
Automation with GNU Make
Running scripts non-interactively
Data Analysis Project workflow
LaTex and Beamer
Pandoc (document converter)
R package “knitr”
R package “rmarkdown”
R package “shiny”
- Reproducibility: The ability to recreate a past analysis, which is
crucial for good science.
- Automation: The ability to rapidly recreate an analysis when data
and/or input changes (as it always does).
- Communication: The ability to clearly present, share, and communicate
your work to others.
- 5% in-class presentation
- 5% github repositories
- 10% lab work and quizzes
- 20% homework
- 10% project 1 (individual)
- 20% project 2 (2 members)
- 30% project 3 (4 members)
This course will focus heavily on in-class participation in addition to
assigned readings from scholarly journals, presentations from guest speakers,
several “feedback” assignments, and weekly blog articles in addition to
regular practice with the software tools listed in the description.
Your persistent cooperation in group work and contributions to the course
will culminate into a collaborative term project. The format will be interactive
and will involve your questions, opinions, and participation.
- Weekly homework assignments are due as posted online.
- Don’t wait until the last hour to do an assignment. Plan ahead and pace yourself.
- After the due date of each assignment, we will discuss the solutions during class.
- No late assignments will be accepted, for any reason, including, but not limited to, theft, extraordinary circumnstances, and your pet’s dietary idiosyncrasies.
- Instead of late HW, I will drop your lowest two HW scores.
Pop Quiz policy
- There will be written pop quizzes during lab (between 4 and 5 approx)
- I will drop the lowest quiz score
- No makeup quizzes (no exceptions)
- There will be three projects (~ one each month)
- If you fail to submit any of the projects, you will fail the course
- I will provide a list of project requirements
- Meeting all requirements gives you a B, but does not guarantee an A
- We are expecting that you add value and personal touch to each project
- Projects 2 and 3 cannot be done individually (you need to COLLABORATE!)
In-class Presentation Policy
- There will be one in-class presentation (teams of 4 members)
- Presentations are based on assigned readings
- Each team will have to prepare some slides and a written report
- The written report must be submitted no later than the day of the presentation
- Each team will have a max of 45 minutes (~ 35 min talk + 10 min Q&A’s)
- All slides have to be publicly shared
- Each team will have one week after the presentation to share their slides
- At the end of the course, the slides must be available in a github repo
- Links to the slides will be included in the course website
- As the course advances, the grading of presentations will become more strict
- No makeup present
- List of Presentations
- You will have to work in teams (presentation, 2nd and 3rd projects)
- All team members must be knowledgeable of other members contributions
- You will be responsible to do peer review and check each other’s work
- It’s possible to have conflicts between team members. If this happends,
you will have to solve them (don’t ask me to solve your problems)
- If you have a lot of commitments (e.g. sports, cal band) come talk to me ASAP
- You should only use email as a tool to set up a one-on-one meeting with me if Office hours conflict with your schedule.
- Use the subject line Meeting Request.
- Your message should include at least two times when you would like to meet and a brief (one-two sentence) description of the reason for the meeting.
- Email sent for any other reason will NOT be considered or acknowledge.
- Do NOT expect me to reply right away (I may not reply on time).
- If you have an emergency, talk to me later during class or office hours.
- I strongly encourage you to ask questions about the syllabus, covered material, and assignments during class time or lab discussions.
- Our conversations should take place in person rather than via email, thus allowing us to get to know each other better and fostering a more collegial learning atmosphere.
Do your own work. Collaborating on homework is fine—but copying is not, nor is having somebody else submit assignments for you. Cheating will not be tolerated. Anyone found cheating will receive an F and will be reported to the Center for the Student Conduct.
If you need accommodations for any physical, psychological, or learning disability, please speak to me after class or during office hours. Please make arrangements in a timely manner (through DSP) so that I can make the appropriate accommodations.