Biostat/Stat 572 and Stat 518
Spring 2014
 Acknowledgement:  Ken Rice!
 Week 1
 1 April 2014: Course overview / searching the literature (Patrick out)
 J. Wakefield: Course Rationale and Expectations
 P. Heagerty: Research / Reading the Literature
 Murphy (2007)  "How to
Read the Statistics Methodology Literature  A Guide to Students",
The American Statistician
 Hamada and Sitter (2004)
 "Statistical Research: Some Advice for Beginners",
The American Statistician
 Schwartz (2008)  on why not knowing everything is an important feeling when doing research.
 Marie Davidian's NCSU course on how to do research
 Korner: How to Write a Part III essay. These are notes for University of Cambridge math postgrads, who (like you) have to write a report based on published literature.
 Links to online citation databases, using your UW access;
 Web of Knowledge, for abstracts, citations, references and links to papers. Covers most scientific areas
 Current Index to Statistics, for bibliographic information in BibTeX format. Only statistics articles, and some books
 Google Scholar, for citations, multiple links to papers, and 'related articles'. Get BibTeX citations by setting your 'Google preferences'
 PubMed, for abstracts, citations, references and links to papers. Covers NIHrelated areas
 arXiv, open access to eprints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics
 MathSciNet, American Mathematical Society (AMS) search tool
 Q: what are the most highly cited
statistics papers for each of the last few decades?
 Assignment:  preparation for Thursday:
 Choose (2) papers from the "Presentation Papers" listed below
and read.
 Send me email by Weds 5pm telling me the papers that you have
chosen.
 Using your paper identify (3) guidelines for a good talk 
use the themes of ORGANIZATION, CONTENT, and PRESENTATION to
label your guidelines if possible.
 Review the "Ken's 2011 slides" below to gain another
perspective  are your identified guidelines apparent in
Ken's slides?
 Goal: To formulate a set of GUIDELINES and SUGGESTIONS.
 Be prepared to discuss results on Thursday.
 3 April 2014: Preparing and delivering a presentation (Jon out)
 M. Meila: Beamer / tools

Ken's 2011 slides (PDF)
 From Navneet H: Numerator Only!  how to only display slide counter and not total

Slides and other material on How To Communicate Graphically

For a primer on drawing graphs in R, see this course

An example Beamer file, with figures (ZIP file)  intended to be selfexplanatory. Made using PCTeX, it may require minor tweaks in order to work on other systems

A LaTeX example featuring DAGs  taken from Ken's 570 notes
 A link to Tikz is HERE
 Example from WenWei Loh:
code and
output
 Simple example of using pstricks to create figure:
code and
output
 From Adam G:
igraph (note that this does a lot more than having some nice plotting algorithms)
 From Adam G:
Rgraphviz (note that this requires installing the graphviz software on your system)
 Presentation Papers

Some examples of good speakers;

An outstandingly good 20 minute talk; Hans Rosling (Swedish Statistician) explains data visualization using mortality vs life expectancy, in 200 countries over 200 years, as a 4minute example. Your talks will be less of a sales pitch, and aimed at a more expert audience  but think about the way he is keeping the audience engaged

A few minutes of Richard Feynman, explaining some connections between Physics and Math. His example is extremely clear, but also note how he paces the material for the audience  not himself

Two similar talks (both are good); Peter Donnelly explains the prosecutor's fallacy to a nonexpert audience. David Spieglhalter discusses the same idea for an evenlessexpert audience, but using more graphics  and in a lot less time
 Assignment:  for your selected paper:
 Search the bibliography of your paper and list the (3) most
highly cited papers that your paper references. (and note the
number of citations for each).
 Summarize the papers that have cited your project paper. Are
there themes (methodologically, scientifically) that are
apparent?
 Also look at citations in the "second generation"  e.g.
citations among papers that cite your project paper. Just
choose a couple and explore the downstream impact of your paper.
 Be prepared to discuss results on Tuesday.
 Week 2
 8 April 2014: Writing Statistical Papers
 M. Meila: Calling C from R, and Cplex optimization.
 P. Heagerty: Statistical papers
 J. Wakefield: LaTeX paper format
 Ken's 2011
Slides (PDF) and a zip file with a BibTeX example

Google Scholar can output BibTeXformat bibliography entires; just set your 'Scholar Preferences', hit 'Import into BibTeX', then cut and paste

Also, Zotero is a (free) Firefox addin that allows straightforward "scraping" of citation information from websites. Having done this, it formats the data for use in other software, e.g. BibTeX

Gopen and Swan (1990) The Science of Scientific Writing is a classic paper on writing clearly

UChicago offers a Sentence of the Week, with great examples of how to make writing clearer. Their writing resources are also good

Strunk and White The Elements of Style is a classic style guide. 'Classic' also means 'old', so don't treat it as gospel  and it is far from perfect. Also, technical writing is often slightly more formal than their 'style'.

The Chicago Manual of Style is also a standard reference, see also The Complete Plain Words

Get easilydigested style tips from this NY Times blog

Paul Brians has an excellent list of nonerrors about which grumpy trolls may be picky. His list of real errors is also a useful reference

Williams and Colomb's point about 'Noun + Noun + Noun' was made (grumpily, but in Science) by Milton Hildebrand (1983). He was subsequently criticized by Baer (1983), who recommended using hyphens where possible

Some fun stuff; TheOatmeal on; thanks to Luis Crouch for these

A fairly definitive note on why to use only one space after a period... which is what LaTeX will do for you automatically

The Mayfield Handbook of Scientific and Technical Writing is a specialized style guide

A checklist of Word Usage in Scientific Writing

Twenty one Suggestions for Writing Good Scientific Papers

Ehrenberg 1982 Writing Technical Reports or Papers (American Statistician) gives good advice on structure, and use of simple language

Andrew Gelman reviews two research articles

Halmos' classic advice on How To Write Math

Lee Notes on Writing Mathematics (from the UW Math Dept)

Knuth, Larrabee and Roberts (1987) Mathematical Writing. This lengthy report also came out as a book

Higham (1998) Handbook of Writing for the Mathematical Sciences, Second Edition, SIAM (partlyviewable through Google Books)
 Krantz (2000). A Mathematician's Survival Guide. American Mathematical Society.
 Krantz (2000). Mathematical Publishing: A Guidebook. American Mathematical Society.
 Krantz (1991). A Primer of Mathematical Writing. American Mathematical Society.
 10 April 2014: Intro Student Presentation [1] (Overview : Motivation
/ Background / Methods intro)
 These talks should be 20 minutes including 5 minutes of questions.
 The goals of the introductory presentation are to introduce the
paper and to motivate the work. A key part of any talk/paper is
showing the audience the need for new methods/theory. This
typically involves both scientific motivation using an example
or data set, and statistical motivation indicating that no
adequate solution exists (e.g. the need for something new!).
Basic elements of the first talk could include:
 Introduce the paper
 Provide motivation for the work (scientific, statistical)
 Review key background literature
 Overview of the methods
 Aaron Baraff Talk
 Amrit Dhar Talk
 Rebecca Ferrell Talk
 Week 3
 15 April 2014: Intro Student Presentation [2]
 17 April 2014: Intro Student Presentation [3] (Jon gone)
 Week 4
 22 April 2014 Intro Student Presentation [4]
 24 April 2014: Finish Talks and More on writing / editing
[ Draft Due: 6 May Intro and Literature Review]
 Your literature review should provide a summary of the major background literature, and should establish motivation for the work in your paper. This may look similar to the lit review in your paper, but your version will probably need to be written for a lessexpert audience, e.g. for those who've had the material up to and including the 570571 (516517), but are not familiar with other material.
The goal of this exercise is to give you practice in this important part of scholarly research, and to develop your background knowledge of the statistical area of focus.
A key part of this exercise is organizing the material; you may find it helpful to summarize major themes in turn (e.g. Empirical Bayes, then measurement error), and then identify novel relationships between these, and/or gaps in the methodological literature (e.g. use of Empirical Bayes for measurement error problems)
Your review should be between 24 pages. Use BiBTeX for reference management and citation within your report.
Bibtex Style Files for Statistics Journals.
Some example literature reviews, from 2010:
 Week 5
 29 April 2014: Update Student Presentation [1] (Patrick out)
 These talks should be 20 minutes including 5 minutes of questions.
 The goal of the "update talks" is for the student to make progress on their paper. In the update talks, students can present on issues that have arisen, and we will allow time for discussion of potential solutions. Please edit your first talk (as needed) and then add new slides that describe your progress. Focus on one or more of the following:Your final presentation should include these elements and therefore the update should represent the logical next step in your work. Please aim to take your allocated 15 minutes, and don't feel the need to review any earlier slides beyond the single slide that reminds us of the basic problem.

Details of the methods in terms of derivation and/or implementation

Details of data simulation that could evaluate the methods

Illustration of the methods using a worked example
 Where you are encountering difficulties
 1 May 2014: Update Student Presentation [2]
 Week 6
 6 May 2014: Update Student Presentation [3] Literature reviews due
 8 May 2014: Update Student Presentation [4]
 Week 7
 13 May 2014: Update Student Presentation [5]
 15 May 2014:
 Return literature reviews and make comments
 Simulations and Computing in R (resources) and extreme coding
 Week 8
 20 May 2014: Final Student Presentation [1]
These talks should be 20 minutes with an additional 5 minutes of questions.
 22 May 2014: More on Writing / Editing (Patrick out)
 Week 9
 27 May 2014: Final Student Presentation [2]
 29 May 2014: Final Student Presentation [3]
 Week 10
 3 June 2014: Final Student Presentation [4]
 5 June 2014: Final Student Presentation [5]