LECTURES: TUE. & THU. 10:30am - 11:30 LOCATION: ACW 206
TUTORIALS: FRI. 2:30 - 5:30 LOCATION: ACW 206
COURSE DIRECTOR: Dr. Joel S. Shore, Professor of Biology
Midterm 1 (20%) Fri 4 Oct ACW 206
Midterm 2 (30%) Fri 8 Nov ACW 206
Exam (50%) Tue, 17 Dec TM Tait 2pm-5pm
All your grades are posted on the link below. The grades listed are your
raw scores on each of test 1 (out of 41) , test 2 (out
of 40) and the final exam (out of 64). I have removed the first 3 digits from
your student numbers and the last digit. So look carefully for your grades. The
“official” letter grades are posted on the official York university
website.
NOTE THAT IF YOU DID NOT WRITE THE
FINAL EXAM A GRADE OF “F” HAS TO BE POSTED UNTIL SUCH A TIME AS YOU
WRITE THE DEFERRED EXAM AT WHICH POINT THE GRADE IS CORRECTED.
Note that if you missed the final
exam, you will be required to fill out a petition to write a deferred exam.
This will mean that you will be writing the deferred (if granted) in the new year. Furthermore, I will be on sabbatical and therefore
the deferred exam will not be handled by me and this will probably not be
advantageous for you.
If you missed the final, please go
to the undergraduate biology office in LSB 1st floor and/or email biology@yorku.ca
FINAL EXAM DETAILS
For the final exam, you may
bring in ONE standard sheet of paper (8.5 inches x 11 inches) with anything you
like written/printed on it, and you may use both sides of that single sheet of
paper.
The final exam will cover all
material since the course began, but will be very heavily weighted towards the
material we have covered in the last two thirds of the course. The focus will largely be on hypothesis
tests of all kinds. The material includes chapters 1 through 17 (excluding
sections I’ve indicated that should be excluded in the course outline
and/or in class) and all problem sets.
SAS will be included as well. (As I’ve stated many times in class,
make certain you conclude all hypothesis tests with a concluding statement
referring to the data and/or means, or comparing observed versus expected,
etc.).
The exam will be 180 minutes in
duration. Roughly 13 questions. Statistical tables
will be provided. Bring your calculator.
Make certain you find the exam room before the morning of the test
so that you are not lost, and end up arriving late.
TEST 2 DESCRIPTIVE STATS FROM PROC
UNIVARIATE
REQUIRED TEXT BOOK
Whitlock and Schluter 2015. THE ANALYSIS OF BIOLOGICAL DATA, 2nd edition. Roberts and Company, Publishers.*
(buy it and begin reading!). We will largely follow the text from the beginning up to and including at least chapter 17. But see below for explicit details of which chapters and sections.
*Note that if you have a copy of the 1st edition of this book, it may suffice, but it is your responsibility to ensure that all the material in the 2nd edition that we cover, is indeed covered in the 1st edition.
TUTORIALS
The tutorials will be devoted to a number of tasks including:
1) Taking up problem sets assigned throughout the course.
2) Learning to use the statistical computing software SAS.
3) Midterm tests will be written during the tutorial period.
4) Dealing with individual problems/questions of students
LEARNING OUTCOMES
Statistics is an extremely important field for biology, and many other disciplines.
By the end of this course students should be able to:
1) Provide a summary of categorical and numeric data using graphical methods and statistics
2) Apply the most powerful hypothesis test(s) to data from a range of biological experiments involving categorical or numeric data.
3) Test the assumptions of various hypothesis tests
4) Interpret the results of the hypothesis tests carried out
5) Carry out the hypothesis tests both by “hand” and using the statistical computer program called SAS
SOME
ADVICE ON HOW TO SUCCEED IN THIS COURSE
1)
ACQUIRE A COPY OF THE TEXTBOOK AND USE IT! YOU ARE
RESPONSIBLE FOR ALL CHAPTERS IN THE BOOK INDICATED BELOW AND ALL MATERIAL IN
THOSE CHAPTERS UNLESS I EXPLICITLY EXCLUDE CERTAIN PAGES/SECTIONS (SEE COURSE
OUTLINE BELOW).
2)
ATTEND ALL LECTURES AND TUTORIALS, AND IF YOU MISS A
CLASS MAKE ABSOLUTELY CERTAIN YOU CONTACT ANOTHER STUDENT(S) AND FIND OUT WHAT
WAS COVERED, AND OBTAIN THEIR NOTES. IT IS YOUR RESPONSIBILITY TO FIND OUT WHAT
WAS COVERED IN YOUR ABSENCE.
3)
AT A MINIMUM, DO ALL THE PROBLEM SETS, AND BETTER, DO
AS MANY PROBLEMS/QUESTIONS AS YOU CAN. I’D HYPOTHESIZE THAT IF YOU DO TEN
PROBLEMS OF EACH KIND, YOU SHOULD DO WELL IN THE COURSE BUT THIS MIGHT VARY
FROM ONE STUDENT TO THE NEXT.
4)
USE THE STATISTICAL PROGRAM (SAS) TAUGHT DURING THIS
COURSE. IT WILL BE A SIGNIFICANT/IMPORTANT TOOL IN THIS COURSE, AND WELL
BEYOND.
5) THIS
COURSE MOVES AT AN ACCELERATED RATE. MAKE CERTAIN YOU KEEP UP OR YOU WILL BE
LOST VERY SOON.
1) INTRODUCTION TO STATISTICS (read chapter 1)
What is statistics?
Populations and samples
Random sampling
Types of data - categorical versus numeric
Explanatory versus Response variables
Frequency and probability distributions
2) DISPLAYING DATA (read chapter 2)
Plotting frequency distributions
Bar graphs, histograms
Contingency tables
Scatterplots for two variables
3) DESCRIBING DATA (read chapter 3)
Sample mean and sample median
Variance and standard deviation
(computational formula)
Quartiles and box plots
Cumulative frequency distribution
Proportions
4) Estimation with uncertainty (read chapter 4)
Estimating a population parameter
Sampling distribution of the estimates
e.g. mean
Standard error
Confidence intervals
5) Probability (read chapter 5 sections 5.1 through 5.8 inclusive)
Probability of events
Mutually exclusive events
Probability distributions
Addition and multiplication rules
Independent events
Probability trees
Pseudoreplication (read pgs 115-116)
6) Hypothesis testing (Chapter 6 & 7)
Null (Ho) versus Alternative (Ha) hypotheses
One versus two-sided tests
Examples
P-value
Type I and Type II errors
Analysing proportions and hypothesis tests using the Binomial distribution
OMIT THE MATERIAL ON CALCULATING CONFIDENCE INTERVALS FOR PROPORTIONS ON PAGES (189-191).
7) Goodness-of-Fit and Contingency tests (Chapters 8 & 9)
X2 goodness-of-fit tests
assumptions
examples
Fitting data to probability distributions
Contingency tests
G-statistic
OMIT SECTION 9.2 ON ESTIMATING ASSOCIATION IN 2X2 TALBES: ODDS RATIOS
8) The normal distribution (Chapter 10)
Ignore normal approximation for the binomial distribution (section 10.7)
The standard normal distribution and probabilities
Normal distribution of sample means
Central limit theorem
9) Student's t-test (Chapter 11 & 12)
the t-distribution
confidence intervals
one- and two-sample t-tests
assumptions
paired t-test
F-test of equal variances
OMIT SECTION 11.5 ON CONFIDENCE LIMITS FOR VARIANCE AND STANDARD DEVIATION
10) Violations of assumptions, transformation and non parametric tests (Chapter 13)
Detecting deviations from normality read section, but won't carry out Shapiro Wilk test for normality.
Transforming data to meet normality assumption
Non-parametric alternatives to t-tests
Ignore chapter 14.
11) Analysis of Variance (Chapters 15)
Single factor ANOVA
Planned versus unplanned comparisons
Fixed versus random effects
(Ignore Nonparametric alternatives pg. 471, but you should know of their existence and when to use them).
12) Correlation and Regression (Chapter 16 and 17)
Chpt 16 only sections 16.1 ( but ignore confidence interval material)
include 16.2, 16.3, 16.4
Chpt 17 only sections 17.1 (ignore confidence interval)
include 17.3 (ignore ANOVA approach).
Correlation coefficient
Linear regression
Estimation of least squares line
Hypothesis test of slope
Assumptions and transformations
13) Recent advances in statistics
Some potentially
useful function/operations in SAS
Computational
formulae for sample variance and standard deviation
I have posted some lectures below as youtube “videos”. These were not made this year
but were made two years ago. They should, however be fairly close to the
lectures given this year.
2. independent sample (2-sample) t-test
3.
F-test to compare two variances
4.a Violations of Assumptions, transformations,
non-parametric tests 1
b. Violations of Assumptions,
transformations, non-parametric tests 2
5. a.
Analysis of Variance, overview, computational equations, example
b. Anova, linear
models, fixed vs random effects, F-tables
c. Anova,
Example, R-squared, apriori test
d. Anova, Tukey
Kramer aposteriori test, variance components
8.
Review of course, which hypothesis test, “advanced” methods
IMPORTANT COURSE INFORMATION FOR STUDENTS (copied
from the Senate Committee on Academic Standards, Curriculum & Pedagogy
BASIC COURSE OUTLINE MODEL)
All students are expected to familiarize themselves with the following
information, available on the Senate Committee on Academic Standards,
Curriculum & Pedagogy webpage (see Reports, Initiatives, Documents)
http://www.yorku.ca/secretariat/senate/committees/ascp/index-ascp.html
·
Senate Policy on Academic Honesty and the
Academic Integrity Website
·
Ethics Review
Process for research involving human participants
·
Course
requirement accommodation for students with disabilities, including physical,
medical, systemic, learning and psychiatric disabilities
·
Student Conduct Standards
·
Religious Observance Accommodation
IMPORTANT DATES
https://registrar.yorku.ca/enrol/dates/fw19
Students who
feel that there are extenuating circumstances that may interfere with their
ability to successfully complete the course requirements are encouraged to
discuss the matter with the Course Director as soon as possible.
Academic
Honesty and Integrity
York
students are required to maintain the highest standards of academic honesty and
they are subject to the Senate Policy on Academic Honesty (http://secretariat-policies.info.yorku.ca/policies/academic-honesty-senate-policy-on/). The Policy affirms the responsibility of faculty
members to foster acceptable standards of academic conduct and of the student to
abide by such standards.
There
is also an academic integrity website with comprehensive information about
academic honesty and how to find resources at York to help improve
students’ research and writing skills, and cope with University life.
Students are expected to review the materials on the Academic Integrity website
at - http://www.yorku.ca/academicintegrity/
Important A note from the Faculty of
Science Committee on Examinations and Academic Standards:
Numerous
students in Faculty of Science courses have been charged with academic
misconduct when materials they uploaded to third party repository sites (e.g.
Course Hero, One Class, etc.) were taken and used by unknown students in later
offerings of the course. The Faculty’s Committee on Examinations and
Academic Standards (CEAS) found in these cases that the burden of proof in a
charge of aiding and abetting had been met, since the uploading students had
been found in all cases to be wilfully blind to the
reasonable likelihood of supporting plagiarism in this manner. Accordingly, to
avoid this risk, students are urged not to upload their work to these sites.
Whenever a student submits work obtained through Course Hero or One Class, the
submitting student will be charged with plagiarism and the uploading student
will be charged with aiding and abetting.
Note
also that exams, tests, and other assignments are the copyrighted works of the
professor assigning them, whether copyright is overtly claimed or not (i.e.
whether the © is used or not). Scanning these documents constitutes
copying, which is a breach of Canadian copyright law, and the breach is
aggravated when scans are shared or uploaded to third party repository sites.
Access/Disability
York
University is committed to principles of respect, inclusion and equality of all
persons with disabilities across campus. The University provides services for
students with disabilities (including physical, medical, learning and
psychiatric disabilities) needing accommodation related to teaching and
evaluation methods/materials. These services are made available to students in
all Faculties and programs at York University.
Student's
in need of these services are asked to register with disability services as
early as possible to ensure that appropriate academic accommodation can be
provided with advance notice. You are encouraged to schedule a time early in
the term to meet with each professor to discuss your accommodation needs.
Please note that registering with disabilities services and discussing your
needs with your professors is necessary to avoid any impediment to receiving
the necessary academic accommodations to meet your needs.
Additional
information is available at the following websites:
Counselling
& Disability Services - http://cds.info.yorku.ca/
Counselling
& Disability Services at Glendon - https://www.glendon.yorku.ca/counselling/
York
Accessibility Hub - http://accessibilityhub.info.yorku.ca/
Religious
Observance Accommodation
York
University is committed to respecting the religious beliefs and practices of
all members of the community, and making accommodations for observances of
special significance to adherents. Should any of the dates specified in this
syllabus for an in-class test or examination pose such a conflict for you,
contact the Course Director within the first three weeks of class. Similarly,
should an assignment to be completed in a lab, practicum placement, workshop,
etc., scheduled later in the term pose such a conflict, contact the Course
director immediately. Please note that to arrange an alternative date or time for
an examination scheduled in the formal examination periods (December and
April/May), students must complete and submit an Examination
Accommodation Form at
least 3 weeks before the exam period begins. The form can be obtained from
Student Client Services, Student Services Centre or online at http://www.registrar.yorku.ca/pdf/exam_accommodation.pdf
Student
Conduct in Academic Situations
Students and instructors are expected to maintain a professional
relationship characterized by courtesy and mutual respect. Moreover, it is the
responsibility of the instructor to maintain an appropriate academic atmosphere
in the classroom and other academic settings, and the responsibility of the
student to cooperate in that endeavour. Further, the instructor is the best
person to decide, in the first instance, whether such an atmosphere is present
in the class. The policy and procedures governing disruptive and/or harassing behaviour
by students in academic situations is available at - http://secretariat-policies.info.yorku.ca/policies/disruptive-andor-harassing-behaviour-in-academic-situations-senate-policy/