Tuesdays and Thursdays, 11 a.m.-12:15 p.m.
217 Gore Hall
Instructor: John McDonald
322 Wolf Hall (office)
Phone: 831-2007 (I rarely check messages, so e-mail is better)
Class web page: http://udel.edu/~mcdonald/statsyllabus.html
Note: Homework assignments and exam study guides without links are not ready yet.
|Date||Day||Lecture topic||Homework due|
Kinds of biological data
Exact binomial test
|Sept. 4||Tuesday||Hypothesis testing and alternate schools of statistics||Homework 1|
|Sept. 6||Thursday||Power analysis|
Chi-square test and
G-test for goodness-of-fit;
Using spreadsheets for statistics
and Fisher's exact test of independence;
Repeated tests of goodness-of-fit;|
|Sept. 20||Thursday||First exam (see the study guide and answers)|
|Sept. 25||Tuesday||Descriptive statistics: Central tendency|
Descriptive statistics: dispersion,
standard error and
Introduction to SAS
testing homogeneity of means
Planned comparisons among means;
Unplanned comparisons among means
Model I vs. Model II anova;
estimating added variance components
|Oct. 23||Tuesday||Second exam (see the study guide and answers)|
|Oct. 25||Thursday||Nested anova|
|Oct. 30||Tuesday||Hurricane Sandy: no school!|
|Nov. 6||Tuesday||Election day: no school!|
Linear regression and correlation
Spearman rank correlation
|Nov. 13||Tuesday||Polynomial regression|
|Nov. 15||Thursday||Analysis of covariance|
|Nov. 20||Tuesday||Logistic regression||Homework 8|
|Nov. 22||Thursday||Thanksgiving, no school!|
|Nov. 29||Thursday||Meta-analysis||Homework 9|
|Dec. 4||Tuesday||Review for exam||Homework 10|
|December 11||Tuesday, 10:30-12:30||Final exam (see the study guide and practice exam one and practice exam two and the answer sheet.)|
This course is designed for biologists who want to apply appropriate statistical tests to their data, and who want to understand the statistical tests that other biologists have used. We will therefore spend little time on the mathematical basis of the statistical tests, focusing instead on how to choose the appropriate test for a given data set, how to design experiments to make them more suitable for statistical analysis, and how to interpret and present the results of statistical tests. While it would be impossible to cover every statistical test ever used by biologists in a single course, we will cover many of those techniques that are commonly used.
At the end of the course, you should be able to determine the correct statistical technique to apply to many biological experiments, and you should be able to apply each technique and interpret the results. You should also be able to recognize experimental designs for which you have not learned the appropriate statistical test, and you should be able to ask intelligent questions when consulting with a statistician about such experiments.
There are no fixed office hours. You can make an appointment by talking to me before or after class or by e-mailing me. If you have questions while studying or doing the homework assignments, feel free to e-mail me or drop by my office.
We will use an online textbook, Handbook of Biological Statistics. It is designed for online use, but if you want to print individual pages, they are formatted to print well (with most of the extra junk, like the sidebar and banner, omitted to save space). If you want to have a printed copy of the whole handbook, you can buy one from Lulu.com for $16 plus shipping, or download a free pdf of the entire thing and print it yourself. Note that I will be publishing a revised, third edition of the Handbook around December 2012, so if you want a printed version, you may want to wait until then.
Attendance is not mandatory, and you will not be graded on your in-class participation. However, I think it will be a lot easier to learn the material if you attend class. Homework assignments and exam study guides will be available from the class web page (http://udel.edu/~mcdonald/statsyllabus.html). If you are absent when a homework assignment is due, please try to turn in the assignment before the next class (you can slide it under my office door, 322 Wolf, if I'm not there). Do not e-mail me your homework assignments; I will not grade them. You must give me your homework assignments on paper.
I try to make the class as interactive as possible, as I find standard lectures to be rather boring. I will therefore call on each of you many times during the semester, whether or not you raise your hand. If this makes you uncomfortable, I can assure you that it would have terrified me when I was in college. Many students have reported on their evaluation forms that being forced to participate kept them attentive in the class and gave them good experience in speaking out. If you do not know the answer to a question, say "I don't know"; sometimes, that's the answer I'm looking for, and even if it's not, I'll try to go to someone else quickly.
I have found that the use of computers during class is distracting for both the students using them and those sitting nearby. You may not use laptops, tablets, smartphones, or other electronic devices during lectures. If I see you using such devices, I'll assume you're looking at porn and mock you accordingly.
Your grade will be based on the following:
15% First exam
25% Second exam
45% Final exam
15% Homework assignments
The grades will not be curved. The points from the
homework and exams will be combined and converted to letter grades as follows:
A 93-100; A- 90-92.9; B+ 87-89.9; B 83-86.9; B- 80-82.9; C+ 77-79.9; C 73-76.9; C- 70-72.9; D+ 67-69.9; D 63-66.9; D- 60-62.9; F 0-59.9.
Students who are less than 3 points below the minimum grade needed for their program (such as an undergraduate biology major with 67 to 69.9 points, or a biology grad student with 80 to 82.9 points) will be given the opportunity to take an incomplete grade and complete an extra credit project. This project will be a lot of work, such as surveying the statistical tests used in a large set of scientific papers and critiquing their correctness. Upon satisfactory completion of the project, you'll get the minimum grade needed for your program (such as C- for undergraduate biology majors or a B for biology grad students). There will be no other extra credit.
The exams will be cumulative. The main emphasis of the exams will be testing your knowledge of what the appropriate statistical test is to use in a particular situation and how to interpret the results. You will not be allowed to use reference books or notes during the exams, and you will not need a calculator. If your native language is not English, you will be allowed to use a dictionary.
A homework assignment is due on eleven Tuesdays. They will be available on the class web page a couple of weeks before they are due. I will not hand out printed copies of the assignments in class.
The homework assignments make up a relatively small portion of your grade, and they will be loosely graded; if you make a sincere effort on all parts of an assignment, you will probably get full credit. Despite this, I suggest that you put a lot of effort into the homework. Many of the skills I hope you learn from this class can only be learned by doing, not by listening to me talking, so your statistical education will be incomplete (and you will struggle on the exams) if you do not do the homework to the best of your ability. Please drop by my office or e-mail me if you need help on the homework.
We are going to use spreadsheets for most of our data analysis. The web page for almost every statistical test will include a spreadsheet that you can download and use with the Windows or Macintosh versions of Excel. As a UD student, you can download Microsoft Office, which includes Excel, for free from UDeploy. The spreadsheets should also work with Calc, part of the free OpenOffice.org suite of programs.
I like using spreadsheets for statistics because most of you already know how to use them, and because they make it easy to combine graphics with the statistical tests. If you're interested in a field that only uses fairly basic statistics, such as molecular or cell biology, the tests that you can do with spreadsheets are likely to be all you'll ever need.
Wherever possible, I've linked to someone else's web page that will perform each statistical test, and you may use them for the homework if you prefer. I found most of these web pages using John Pezzullo's excellent list of Interactive Statistical Calculation Pages, which is a good place to look for information about tests that are not discussed in this course. For most tests, the web page version is not as easy to use as a spreadsheet, and many web pages only handle limited sample sizes. Some web pages, however, do tests that would be difficult to set up on a spreadsheet.
Each of my web pages about a statistical test will also include instructions for performing the statistical test using SAS. SAS is a powerful but user-unfriendly statistical package that can do statistical analyses that are far beyond the abilities of spreadsheets. While I don't expect you to become an expert in SAS, I'm going to try to teach you some of the basics this fall. Most of the homework assignments will require that you do each statistical test two ways, once with a spreadsheet or web page, then again with SAS. If you have problems with SAS, do not stay up all night struggling with it. Instead, send me an e-mail with as much information as possible (your SAS program, the error messages you're getting, a picture of your computer with smoke coming out of the back) and I'll try to help you. If there isn't time for me to respond before the homework is due, put this information in your homework assignment.
If you already know another comprehensive statistical program, such as R, SPSS, or Stata, you may use it on the homework assignments to check your answers. However, you will still be required to use spreadsheets and SAS for the homework. This is because I do not know anything about R, SPSS, Stata, etc. and can't help you with them.
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This page was last revised December 12, 2012. Its URL is http://udel.edu/~mcdonald/statsyllabus.html