PLNT*6170 Statistics in Plant Agriculture

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The following description is for the course offering in Winter 2019 and is subject to change. It is provided for information only. The course outline distributed to the class at the beginning of the semester describes the course content and delivery, and defines the methods and criteria to be used in establishing the final grades for the course.
 

The application of statistical techniques to research in plant agriculture. SAS is the software used to perform data analysis. Emphasis is placed on statistical principles, the design of experiments, the testing of hypotheses, and communication of findings to other scientists.

Instructors:

Teaching Assistant:

Credit Weight:

0.50

Course Level:

  • Graduate

Academic Department (or campus):

Department of Plant Agriculture

Campus:

Guelph

Semester Offering:

  • Winter

Class Schedule and Location:

Please refer to WebAdvisor for class schedule and location.

Learning outcomes:

This course is designed to contribute to your achievement in three of the five university-wide learning outcomes: Critical and creative thinking, Literacy, and Communication. 

By the end of this course, students should be able to:
  1. Understand and apply classical inference involving confidence intervals and hypothesis testing
  2. Explain and apply methods to compare treatments
  3. Apply and interpret variance partition models
  4. Recognize and apply various experimental designs
  5. Demonstrate the ability to convey statistical results to other researchers

Lecture Content:

  • SAS 9.4 for Windows [or SAS University Edition]
  • Distributions, hypotheses tests, power, t-tests
  • Goodness of fit, contingency tests, odds ratio, log odds, meta analysis
  • Research design principles: replicates, power, sample size; Modelling: fixed vs random effects, CRD, RCBD; Means comparisons
  • Correlation, effect size, linear and non-lin regression, BLUE vs BLUP
  • Regression in ANOVA
  • Tests of assumptions; Residual analyses; Covariance structures; Non-Gaussian variable; GLMMs
  • Experimental error: How can we control it? Covariates; Experimental designs with blocking
  • Experimental Designs: Split-plot; Split-block; Factorial; Repeated Measures
  • Experimental Designs: Incomplete Block; Fractional Factorial; Response Surface
  • Multiple Regression; Time Series analysis; Area under the curve
  • Multivariate analyses (Manova, path, factor, PCA, cluster)
  • Research Data Management: Where to from here?
Labs & Seminars:

There are no labs or seminars scheduled for this course.

Course Assignments and Tests:

Assignment or Test Contribution to Final Mark Learning Outcomes Measured

Online quiz 1

5% 1-4
Online quiz 2 5%

1-4

Online quiz 3 5%

1-4

Data analysis 1 20%

1-5

Critical Review 20%

1-5

Data analysis 1 20%

1-5

Final project report 25%

1-5

Additional Notes:

On-line quizzes. These will be conducted in Courselink. They will be available beginning 6:00 pm on the Monday and will close 11:30 pm on the Wednesday. You are allowed up to two attempts to write each quiz. Your grade will be the average of all attempts.

Data Analysis reports. The report, including a copy of the SAS result window (as a pdf file) is to be uploaded to the courselink dropbox by 8:30 am of the due date. The report and code (not the SAS result file) are also to be submitted in paper format at the beginning of the lecture for your section.

Course-based Masters Students:  If you are electing to critique a paper for the final project, submit a copy of the journal article on 11 February for pre-approval by the instructor.

AUDIT STUDENTS:  To receive an “Audit” from this course, you are required to:

  1. Complete each of the quizzes, and;
  2. Submit one of the two data analysis reports, and;
  3. Submit the critical review of the journal article.

Audit students will not submit a final project.

Final examination:

There is no final examination scheduled for this course.

Course Resources:

Required Texts:

Bowley, S.R. 2015. A hitchhiker’s guide to statistics in biology. Generalized Linear Mixed Model Edition. Plants et al., Guelph ON.  ISBN 978-0-9685500-4-5

Recommended Texts:

Not applicable.

Lab Manual:

Not applicable.

Other Resources:

CourseLink will be used to distribute assignments, data files, information, and other materials associated with the course. You will also use this to submit the pdf copy of your SAS analyses for the graded reports. For each week, there are three to five Self-Assessment questions available for you to assess your understanding of the previous week’s material (select “Self Assessment” from the menu ribbon). There are also three graded quizzes during the term; these will be conducted on-line via CourseLink.

Note that if you are in arrears regarding tuition fees, your access to the CourseLink website will be unavailable until you have settled matters with the Registrar’s Office.

Marks will be collated in Courselink throughout the semester. It is your responsibility to review these grades and report if there are any discrepancies. Keep paper and/or other reliable back-up copies of all in- and out-of-class assignments: You may be asked to resubmit work at any time.

SAS Software

To perform the statistical analyses in this course you will be required to use SAS. Either the Licensed SAS version 9.4 or the free version called SAS University Edition will be suitable for the analyses required. Both contain the SAS/STAT 14.2 release. Note that it is your responsibility to acquire access to the SAS software.

Many of the research labs have the Licensed SAS version installed in the computer pools for their research teams. The software is also on all computers in the Learning Commons computer lab (Library). We have also placed it on the open-access computers located on the third floor CRSC outside the elevators and Bovey Rm 3109. The computers in CRSC 121-A will also be available for use by the course Thursday afternoons. Students in the Dept. Animal Biosciences also have access to the licensed version on their Departmental server.

Mac Users: The SAS University Edition works fine on this platform and the price is right ($0) but you will require a program such as VMware Player.

It is not necessary for this course, but if you want to have a copy of the full edition on your own laptop (Windows OS) you will have to make arrangements with CCS and purchase a license code for the year. Note that only the Windows 64 bit version has been licensed by the University. Before doing so, check with your advisor in case he/she has purchased a renewal for a lab license for their research group. 

Field Trips:

Not applicable.

Additional Costs:

Not applicable.

Course Policies:

COURSE CONSTRAINTS

There is a ban on the use of writing services and statistical analysis services for all reports submitted in this course.

Grading Policies:

The reports for the week 3, 5, 6, and 8 analyses will be graded out of 10 using the following rubric:

Item Score

Required components (report, code, SAS result pdf)

3

Application of methodologies

5

Accuracy and clarity

5

Interpretation of results

5

Adherence to specified style and format

2

 
The critical review assignment will be graded out of 20 using the following rubric:
 
Item - based on the checklist provided Score
Objective

 

1

Experimental Design

5

Sample Size

2

Statistical Procedures

5

 Presentation of Results

3

Publishable?

2

Adherence to specified style and format

2

Quizzes: Quizzes will be available on-line through CourseLink between the time-period: 6 pm Monday to 11:30 pm Wednesday. To receive a mark, you must complete the quiz during this time interval.  You are allowed up to two attempts to write each quiz. Your recorded grade will be the average of all attempts. You do not require access to SAS in order to complete the quiz.

Analysis Reports: All three sections must be submitted electronically as pdf files via the CourseLink Dropbox by 8:30 am on the due date. In addition, Sections 1 and 2 of the weekly Analysis Reports must be submitted in paper format at the beginning of class on the due date.

Final Project: To be submitted both electronically via the CourseLink Dropbox and in paper format at the beginning of the last class meeting. Late reports will not be accepted after the dropbox closes and these will receive a 0 grade.

PDF format: Electronic files uploaded to CourseLink must be in a portable document format (*.pdf). If you upload your report file in a different format than specified, your assignment will be considered "not submitted." Late reports will not be accepted after the dropbox closes/after the beginning of class and will receive a 0 grade.

See the last section: Additional Course Information, for details about style and format of the reports.

CONFLICT WITH A DUE DATE:

If a due date for an assignment / quiz conflicts with a scheduled academic activity such as attendance at a conference, an activity involving a research project, or personal issues such as medical procedures, jury duty, etc., email me ahead of time so we can make alternate accommodation.

Course Policy on Group Work:

It is anticipated that you will work on the weekly projects in study groups, however, the assignments and reports you submit for grading must be independent and document only your work.

Plagiarism will be strongly suspected if two or more students submit individual projects that have identical or substantially identical components. Tables, figures, paragraphs in reports should reflect your own efforts, not be copies or essential derivatives of work performed by someone else. See “Academic Misconduct” below for the procedures that are followed if this arises.

Course Policy regarding use of electronic devices and recording of lectures:

Electronic recording of classes is expressly forbidden without the prior consent of the Instructor. This prohibition extends to all components of the course, including, but not limited to, lectures, seminars, and lab instruction. When recordings are permitted they are solely for the use of the authorized student and may not be reproduced, or transmitted to others, without the express written consent of the Instructor.

The instructor will be using an iPad with Doceri to record one of Monday’s classes (likely the 8:30 session); this will capture his voice and the presentation visuals displayed during the session. The podcast will be uploaded to a Youtube site and a link to the recording will be posted in Courselink  under “Contents.”

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Other Course Information:

I. STYLE GUIDE

Tables and figures should be suitable for submission to one of the refereed journals of the Agricultural Institute of Canada (AIC) such as the Can. J. Plant Sci. or the Can. J. Anim. Sci. The citation format is Council of Science Editors (CSE) Name-year. Title, figures, tables and footnotes (if any) should be self-explanatory so that one can interpret what is being presented without one having to refer to the methods/results. Titles need to be brief but sufficiently detailed to explain the data and statistical analysis.

Here is a link to the AIC style guide: http://www.aic.ca/journals/pdf/Instructions/Operations_Manual_Revised_2012.pdf

See pages 7 through 10, and 12 of the style guide pdf. Don’t rely on a current article as a reference guide for the tables to submit to PLNT*6170. Focus on this phrase: Figures and table should be self-explanatory so that one can interpret what is being presented without having to refer to the methods/results. Unfortunately, many published papers contain tables that have lots of wasted real estate in which one could incorporate one or two words or phrases, or a brief footnote to provide greater clarity, especially related to the statistics. 

Figures & tables are to be suitable for submission for review of a manuscript. There are two notable exceptions for the assignments for this course: 1) Do not turn on line numbering; and, 2) Place the title of a Figure on the same page as the figure image – do not place the Figure title on a separate page (as you would typically do for a manuscript).

II. DATA ANALYIS REPORTS

There is an experiment to analyze each week but only two reports will be submitted for grading. For each report there are three Sections to submit electronically to the CourseLink dropbox as pdf files: 1. The report text including requested Table/Figure(s); 2. The SAS statements that you used for the analysis; and, 3. A copy of the SAS output window for your analysis. Sections 1 and 2 are also to be submitted in paper format at the beginning of class on the due date. A staple in the upper left corner is all the binding that is required.
 
The DO NOT list: Don’t include a literature review, don’t put on a fancy cover, and don’t use colours. The reports, including figures, must be in grey-scale only. You are neither to do a literature review nor to create a manuscript. Only the requested figures/tables and text will be read/graded. You will be provided a guide to each individual analysis and what to include in the report.

III. CRITICAL REVIEW OF A JOURNAL ARTICLE

Throughout your student and research career, you will read a large number of journal articles. Most of us will read these and never question the content or critically evaluate the content. The goal of this assignment is for you to read one of the journal articles listed on CourseLink, and to take a critical look at it. Place yourself as the reviewer of the journal and your goal is to decide whether the article merits publishing or not.

Based on a checklist, adapted from Maindonald and Cox (1984 N.Z.J. Agr. Res. 27:597-610), review the article with these questions in mind:
1. Is the purpose (objective) of the study and the hypotheses tested sufficiently described?
2. Is the experimental design adequate in: a) its description; b) information relevant to analyzing the results; and c) the assignment of treatments and choice of sample?
3. Does the experiment seem adequate in sample size and was the design appropriate?
4. Are the statistical procedures a) described and referenced; b) appropriate; and c) consistently applied?
5. Is the presentation of statistical material clear and appropriate in the text, tables, and figures?
6.From the statistical viewpoint, is the information provided and presentation of the results of this experiment of acceptable standard to be published? What needs to be done to strengthen it?
7. Comment on any statistical issues not covered by the above questions.
 
The critique is limited to a maximum 5 page typed (double spaced) report. A copy of the critique with the citation of the article reviewed must be submitted for grading. Your critique should answer all of the questions in the checklist above, and conclude with a statement whether you would publish the article or not, and 1 recommendation to improve the article.
Upload a PDF copy of your review to the courselink dropbox by 8:30am of the due date, and submit a printed copy at the beginning of your class.

 

A) PhD STUDENTS and THESIS BASED MASTERS STUDENTS

The final assignment is a maximum 5 page typed (double spaced) report detailing an experiment you are proposing to conduct, or are in the process of conducting, as part of your thesis research. The purpose of the project is to provide you an opportunity to apply the three major principles that the late Gertrude Cox (North Carolina State) emphasized for conducting experiments:

1. The experimenter should clearly set forth his or her objectives before proceeding with the experiment.

2. The experiment should be described in detail.

3. An outline of the analysis should be drawn up before the experiment is started.

The report must be written in scientific format and must:

1) Introduce the problem and the background information motivating the experiment under consideration;

2) Define the hypothesis and objectives of the experiment;

3) Detail the experimental design and the layout of the experiment;

4) Outline the statistical analysis and list the SAS statements needed to obtain the analyses; and

5) Indicate the assumptions required to make the analysis valid.

It is acceptable, and you are encouraged, to include one or two figures and one or two tables as part of the report. Tables, figures, references, the SAS statements, and cover pages will not be included as part of the “page-count.”

Grades will be assessed using the criteria listed for the assignments. Note that a penalty of twenty marks (out of 100) will be imposed for each page over 5 pages of text.

B) COURSE-BASED MASTERS STUDENTS

If you are involved with a research experiment as part of your studies, submit the report described above. Otherwise you will do a critique of a recently published article for your final report.

The purpose of this assignment is to give you the opportunity to conduct a critical review of the design, analysis, explanation, and presentation of results of an experiment. You are required to select a journal article published within the last year and critique the use of statistics for the experiments presented in the article. The article must be relevant to your field, must not have been published in any of the American Society of Agronomy journals (ie. Crop Sci., Agron. J., etc.), and must be pre-approved by the course instructor.

The following checklist, adapted from Maindonald and Cox (1984 N.Z.J. Agr. Res. 27:597-610), is provided to assist you with the critique:

1. Is the purpose (objective) of the study and the hypotheses tested sufficiently described?

2. Is the experimental design adequate in: a) its description; b) information relevant to analyzing the results; and c) the assignment of treatments and choice of sample?

3. Does the experiment seem adequate in sample size and was the design appropriate?

4. Are the statistical procedures a) described and referenced; b) appropriate; and c) consistently applied?

5. Is the presentation of statistical material clear and appropriate in the text, tables, and figures?

6. From the statistical viewpoint, is the information provided and presentation of the results of this experiment of acceptable standard to be published? What needs to be done to strengthen it?

7. Comment on any statistical issues not covered by the above questions.

The critique is limited to a maximum 5 page typed (double spaced) report.  A copy of the critique along with a printed copy of the journal article must be submitted for grading. The critique will be assessed as outlined for the assignments. Note that a penalty of twenty marks (out of 100) will be imposed for each page over 5 pages of text. 

IV. CLASSROOM ETIQUETTE

Questions:Do not hesitate to ask questions during class. If there is something that is unclear, confusing, or needs further explanation, please ask!

Disruptive behaviour:You are expected to avoid behaviour that interrupts the learning environment for fellow students. This includes, but is not limited to, use of cell phones and use of electronic devices for purposes unrelated to the course. Turn your cell phone off; disable movie & video feeds, and remove offensive pictures from your desktop/screen saver.

V. WEEKLY ANALYSES

The experiments used for analyses each week are designed to sequentially build your knowledge and skills for data analysis and interpreting results. So, even though there are analyses that are not submitted for grading, you still need to work through them. I hold the Help Sessions on Thursdays since this gives you a few days to work on the analysis yourself and gives you a few days thereafter to finalize your report.

There are a number of components from previous weeks you will need to integrate into later assignments. Indeed, I will be expecting some of these to be included without the need to tell you to do so. The Help session on Thursday will focus on giving assistance with the new techniques for that week –not items that were covered in previous weeks.

Sometimes the analysis hurdle is a SAS coding problem. In case you have a conflict attending the help session (such as commuting distance and weather), I can provide a limited degree of help via email so long as you attach your code/editor file (ie. the ____.sas file) to your email.

University Policies

Academic Consideration

When you find yourself unable to meet an in-course requirement because of illness or compassionate reasons, please advise the course instructor in writing, with your name, id#, and e-mail contact. See the academic calendar for information on regulations and procedures for Academic Consideration:

Academic Misconduct

The University of Guelph is committed to upholding the highest standards of academic integrity and it is the responsibility of all members of the University community, faculty, staff, and students  to be aware of what constitutes academic misconduct and to do as much as possible to prevent academic offences from occurring.

University of Guelph students have the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff and students have the responsibility of supporting an environment that discourages misconduct. Students need to remain aware that instructors have access to and the right to use electronic and other means of detection. Please note: Whether or not a student intended to commit academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of assignments does not excuse students from responsibility for verifying the academic integrity of their work before submitting it. Students who are in any doubt as to whether an action on their part could be construed as an academic offence should consult with a faculty member or faculty advisor.

The Academic Misconduct Policy is detailed in the University Calenders:

Accessibility

The University of Guelph is committed to creating a barrier-free environment. Providing services for students is a shared responsibility among students, faculty and administrators. This relationship is based on respect of individual rights, the dignity of the individual and the University community's shared commitment to an open and supportive learning environment. Students requiring service or accommodation, whether due to an identified, ongoing disability or a short-term disability should contact the Student Accessibility Services (SAS), formerly Centre for Students with Disabilities (CSD), as soon as possible.

For more information, contact CSD at 519-824-4120 ext. 56208 or email sas@uoguelph.ca or visit the Student Accessibility Services website: http://www.uoguelph.ca/csd/.

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Your responses will not affect your grade.  Course evaluation data are distributed to individual instructors after final grades have been submitted to the Registrar, following the completion of each academic semester.

Please be honest, respectful, constructive and thorough.  Instructors and review committees place great value on student course ratings and read all comments provided in course evaluations. It is helpful to provide comments on the strengths of the course, in addition to the areas for improvement.  Please refrain from personal comments unless they relate to teaching and learning.

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