Section outline

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  • Friday, January 10, 2020; 10:30 AM - 12:00 PM

    Lecture:

    Two disease needle stick example, independence, Bayes theorem, review of sensitivity, specificity, NPV, PPV, binomial risk models, expectation, variance, entropy, likelihood, partition of variance, variance inflation, conditional expectation.

    Faculty:  Travis C. Porco

    Location:      Mission Hall 1108

    • Required Reading: 

      Links will be update later tonight 1/6/2020

      Binomial distribution

      Conditional probability

      Independence

    • Optional Reading:

      Introduction to Probability

      Books available to read at Sarah's desk (2655) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

      [The books haven't arrived yet, but will arrive next week.]

    • SarahNotesLecture1 File
    • Calculus Review -- Read by next class if needed File
      Not available unless: Your ID number contains 02

    • Assignment:

      There are 11 total homeworks due Fridays before class. Homework can be turned in to Rae or by email to rae.wannier@ucsf.edu (cc travis.porco@ucsf.edu). For all homework assignments, please hand-write equations or typeset them using Latex or Word equation editor (do not turn in unformatted inline equations, e.g. x^2 + y^2 =1). 

      Grading: 80% and above is an A. One letter grade off per week for late homework (i.e. homework greater than zero but fewer than 7 days late gets a maximum of 80%, homework greater than 7 days late and less than 14 days late gets a maximum of 70%, etc.). 

      Special Instructions for this assignment:

      There are 20 problems, which was too long last year. The completion of 9 required questions is for full credit, completion of the remaining questions will be extra credit.

      Required problems: 2, 4, 5, 6, 9, 11, 12, 19, 20

      Note on problem 3: You should be able to get both an upper and lower bound for the specificity. You should be able to write f as a function of theta, phi, and s. Then s can range from 0 to 1. Plugging in 0 and 1 for s should correspond to your lower and upper bounds for f since f is linear and increasing in s.

      This assignment is due January 20th. 

      Also, send Travis (travis.porco@ucsf.edu) an email briefly introducing yourself and topics you're most interested in. 

    • homework and coursenotes1 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, January 17, 2020; 10:30 AM - 12:00 PM

    Lecture:

    Likelihood, conditional independence, conditional variance, Markov models

    Faculty:  Travis C. Porco

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2655) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment:

      There are 11 total homeworks due Fridays before class. Homework can be turned in to Rae or by email to rae.wannier@ucsf.edu (cc travis.porco@ucsf.edu). For all homework assignments, please hand-write equations or typeset them using Latex or Word equation editor (do not turn in unformatted inline equations, e.g. x^2 + y^2 =1). Please complete all numbered problems in the document below. 

      Grading: 80% and above is an A. One letter grade off per week for late homework (i.e. homework greater than zero but less than 7 days late gets a maximum of 80%, homework more than 7 days late and less than 14 days late gets a maximum of 70%, etc.). 

    • homework and coursenotes2 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, January 24, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Correlation, geometric distribution, generating functions, AR1

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2655) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment: 

      Do problems 1-6,

      Optional extra credit: 

      Show the following: If Y=kX + C, then p(X,Y)=1. 

    • homework and coursenotes2 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, January 31, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Forecasting, data, Holt-Winters, geometric distribution, negative binomial distribution

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2655) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment:  final version. 

      Exercises Assigned: 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14. (skip questions 7, 10 and 13)

      Also do questions 7-9 from Lecture 2 if you have not already done so.

      Due in class 2/9/18

    • homework and coursenotes3 File
    • homework and coursenotes4 File
    • gonorrhea data File
      Not available unless: Your ID number contains 02

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, February 7, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2655) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Resources:

      Please read the articles below in preparation for class on Friday, Feb. 9th.

    • SarahNotesLecture4 File
    • SarahNotesLecture5 File
    • Blumberg et al., 2015 File

      Assessing Measles Transmission in the United States Following a Large Outbreak in California

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455058/

    • Ackley et al., 2017 File

      Genotype-Specificc Measles Transmissibility: A Branching Process Analysis

      https://academic.oup.com/cid/advance-article/doi/10.1093/cid/cix974/4598333

    • Assignment:   

      Lecture 4: Exercise 6
      Lecture 5: Exercises 0-4

    • homework and coursenotes4 File
    • homework and coursenotes5 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, February 14, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2667) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Resources:

    • Rae Notes Lecture 6 File
    • SarahNoteLecture6 File

    • Assignment: 

      Course Notes #6 - 2, 3, 4

      Additional Problem: (i) Posit the size (volume) of a bacterium (ex. E. coli) by an order of magnitude. (ii) Calculate the volume of the earth (imagine it to be spherical).  (iii) The bacterium E. coli doubles every thirty minutes.  Supposing there are no limits on food, space, mixing, death, etc., how much time will it take for one E. coli bacterium to fill up the same volume of space as the earth?

    • homework and coursenotes6 File
    • homework and coursenotes6 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, February 21, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2667) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment: 

      course notes 6: 5, 6 (turn in five graphs), 7 

      Extra problem: Roll your own chain binomial model!

      Choose a new chain binomial model that is in some manner different than the either the Reed-Frost process or the Greenwood model.  In the Reed-Frost chain binomial process we use a binomial with x(t) susceptible and Y(t) infectives with risk of infection r(t)=1-(1-p)^Y(t).  If instead, r(t)= q when y is greater than zero and zero otherwise, this is the Greenwood chain binomial model.  

      Make up your own chain binomial model with a new risk function.  Discuss the interpretation and implications of your model.  Do you want your risk to increase, decrease, increase more slowly vs. the Reed-Frost model?  Where might your model be relevant in practice?

    • homework and coursenotes6 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, February 28, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2667) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment: 

      Course Notes 7:  1, 3, 4, 5, 6   

      Additional Problem: For g(u) = e^(λ(u-1)) = e^(-λ) e^(λu) :  Prove that the variance of X is λ , i.e. var(X) = λ.

    • course notes and homework 7 File

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, March 6, 2020; 10:30 AM - 12:00 PM

    Friday, March 2, 2016; 8:45 AM - 10:15 AM

    Lecture
    Lecture narrative description here

    Faculty:  Travis Porco

    Location:      Mission Hall 1108

    • Optional Reading:

    • Assignment: 

      Course Notes 8: 1-3, 5. (skip 4)

    • Lecture and Course Notes 9 File
    • homework8 File

  • Friday, March 13, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2667) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Assignment: none

    • Assignment Due Date:  

    • homework and coursenotes9 File

  • Friday, March 20, 2020; 10:30 AM - 12:00 PM

    Lecture:
    Lecture narrative description here

    Faculty: 

    Location:      Mission Hall 1108

    • Optional Reading:

      Books available to read at Sarah's desk (2667) at Mission Hall, please do not remove from Mission Hall & return to desk when not reading.

      • An Elementary Introduction to the Theory of Probability (Dover Books on Mathematics)
      • The Theoretical Minimum: What You Need to Know to Start Doing Physics, calculus chapter, if calculus review needed

    • Final Assignment:

      What is the scope and role of mathematical modeling in infectious disease epidemiology? What are the strengths and weaknesses of the approach? For what sort of public health questions might mathematical modeling be useful?  

      256 word limit - due Friday, March 31st at 9 am