STA 312: Survival Analysis

University of Toronto Mississauga, Spring 2019

http://utstat.toronto.edu/~brunner/312s19

Lecture: Monday 11:10 - 1:00 and Wednesday 11:10 - 12:00 in NE 1190

• Instructor: Jerry Brunner
• Office: 3028 Deerfield Hall
• Phone: 905-828-3816
• email: brunner[at]utstat.toronto.edu
• Office Hours: Monday 1:10-3:00 and Wednesday 12:10-1:00

Note: Jerry does not read his email every day. It is much more efficient to talk with him before or after class, or during office hours.

Tutorial: Monday 7:10-8:00 p.m. in Davis 2080

• Instructor: Eman Abo Alya
• Office: CC2110
• email: eman.aboalya[at]mail.utoronto.ca
• Office Hours: Monday 6-7

Text: Applied survival analysis using R by Dirk F. Moore. It is a free download from the U of T library. Additional reading material is available on the course home page.

Topics: Maximum likelihood, Censoring, Survival function, Distributions, Hazard and cumulative hazard function, Parametric analysis for a single sample, Life tables, Kapan-Meier estimates, Parametric regression for censored data, Proportional hazards model, Time-varying covariates. R will be used for computation.

Prerequisites: STA260. STA302 is recommended.

Grading: Marks will be based on equally weighted weekly quizzes given in tutorial, and a comprehensive final exam. The quiz average counts for 60% of the mark, and the final exam is worth 40%. Quizzes will be given in tutorial every Monday starting January 14th. Quiz dates are Jan. 14, 21, 28 Feb. 4, 11, 25, March 4, 11, 18, 25 and April 1 -- for a total of 11 quizzes. The lowest quiz mark will be dropped.

In spite of the mark weighting scheme above, a good performance on the final exam can save a student from failing the course. Suppose your final average including the final exam is less than 50%. If your mark on the final exam is at least 70%, or your mark on the final is at or above the class median, then you get a mark of 50% for the course. This rule is intended to give hope to students who have messed up on the quizzes, and encourage them to study for the final exam.

There will be an assignment for each quiz. The knowledge you need to do each quiz is a subset of the knowledge you need to do the corresponding assignment. Some (most) of the assignments include a computer part. You will bring printouts to the quiz and answer questions based on the printouts. Possibly, one of the quiz questions will be to hand in a printout. The non-computer parts of the assignments are just to prepare you for the quizzes; they will never be handed in.

Policy for missed work: If you miss a quiz, the mark is zero. However, your lowest quiz mark will be dropped. If you miss a quiz with a valid excuse, your mark on the final exam (out of 10) will be substituted for the missing quiz mark, and the lowest remaining mark will still be dropped. If you believe you have a valid excuse for missing term work, please see Jerry (not the TA) in person during office hours or before or after class.

What is a valid excuse? Here are some guidelines. If you miss a quiz for medical reasons, you must submit a University of Toronto Medical Certificate (not just a note), available at

http://www.illnessverification.utoronto.ca.

The certificate must include the statement that you were unable to write the test or quiz for medical reasons. If the certificate does not clearly state that you were unable to function, the excuse will not be accepted. Documentation must show that the physician was consulted on the day of the quiz, or on the next day. A statement merely confirming a report of illness made by the student is not acceptable.

On the other extreme, automotive breakdown or other transportation problems are never valid excuses. If you miss term work because you are taking another class at the same time as this one, that is not a valid excuse. The printer jammed, my dog ate it, etc. fall into the same category. If the University is officially open, weather is a valid excuse only if more than 50% of the class miss the quiz.

Academic Honesty: It is an academic offence to present someone else's work as your own, or to allow your work to be copied for this purpose. To repeat: the person who allows her/his work to be copied is equally guilty, and subject to disciplinary action by the university.

The main rule is don't copy, and don't let anyone else copy from you. You are expected to do the work yourself, and then perhaps compare numerical answers after you have done so. A good rule is to never help someone who hasn't started yet.

Here are some guidelines that apply to the computer assignments. If there is a problem with plagiarism, it will probably happen here, since computer printouts may be handed in.

• In this course, it is always okay to use R program code that is presented in lecture, tutorial, or posted on the class website. Use it any way you like; you are responsible for the results. If your work is very similar to what is presented in lecture, office hours or suggested readings, that is okay.
• It is surprisingly easy to detect copying, and copying from other students is not allowed. If two students have computer work that is excessively similar, but not similar to what was presented in lecture or office hours, that is evidence of cheating. Of course it's easier to detect if the work is also wrong.
• For some quizzes, you will be asked to bring your printouts to the quiz in tutorial; maybe you will hand them in, and maybe you will use them to answer questions. Never, ever, bring a copy of somebody else's printout, or allow anyone to have a copy of yours. Your "friends" may ask you. You are expected to refuse.
• If you allow anyone to have an electronic copy of your computer work, for any reason, you are not only guilty of an academic offence, you have lost your mind. This definitely applies to photographs.
• On the other hand, you are allowed to compare numerical answers as long as you do not see other students' code. Suppose that several students are sitting together and one says "What did you get for theta-hat-3? I got 7.29." Three students nod and say yes, and another groans and reaches for his laptop. This is all good.
• If you are asked to hand in your printout, your name and student number should be on the printout. You are allowed to write your name and student number on the printout in advance, but do not write anything else on your printouts in advance.
• This should be obvious, but if you are asked for a number from your printout and you don't have a printout, do not answer the question and pretend you remembered the number. If you do, you will be charged with an academic offence.
• This also should be obvious, but you are not allowed to put answers or any other material related to the non-computer questions in comment statements, or otherwise cause such material to appear on your printout.
• You are also not allowed to put interpretation or explanation of results on your printout. If you wish, you are allowed to put question numbers, or even a copy of the question that the analysis is trying to answer. The rule is that you may not put anything on the printout that you could not have typed before seeing the results.
• Direct copying of computer code from the internet (other than from the class website of STA312H5 2019) is prohibited. An exception is R functions (for example Wtest) that Jerry has posted online and used in lecture.
• It is acceptable to get help with your computer assignments from someone outside the class, but the help must be limited to general discussion and examples that are not the same as the assignment. As soon as you get an outside person to actually start working on one of your computer assignments, you have committed an academic offence.
• Be particularly careful about paying outside "tutors" to do the computer assignments for you. If they solve the problems (or otherwise obtain solutions) for money and give you the answers with or without explanation, you are guilty of an academic offence. If they are students, they are also guilty, and face possible expulsion from the university for a first offence if they are accepting money.
• Don't copy, and don't let anyone copy from you. If we catch you, you will get in big trouble. Over and above trouble from the university, you do not want to receive a visit from my Associates. They know where you live.

If this is not clear enough, the latest version of the student handout "How not to Plagiarize" is available at http://www.writing.utoronto.ca/advice/using-sources/how-not-to-plagiarize The Academic Regulations of the University are outlined in the Code of Behaviour on Academic matters, which can be found in the Arts and Science Calendar or on the web at http://www.governingcouncil.utoronto.ca/policies/behaveac.htm.

Accessibility Needs: We are committed to accessibility. If you require accommodations for a disability, or have any accessibility concerns about the course, the classroom or course materials, please contact Jerry or Accessibility Services (visit http://www.utm.utoronto.ca/accessability or email accessconfirm.utm@utoronto.ca) as soon as possible.