Overview of course

Note: Lectures and exercises classes are both for master students enrolled in the course Applied Statistics, block 2, 2020 and for PhD students on Statistical methods for the Biosciences I, block 2, 2020.

Course responsible / exercises: Phillip Bredahl Mogense (pbm@math.ku.dkk)
Lectures: Bo Markussen (bomar@math.ku.dk)
Lectures are given online using Zoom on Wednesdays starting on November 18 at 9:00 AM. (link to join lectures)
Exercise classes are held online using Zoom on Wednesdays starting on November 18.
The exercise sheets and the lecture slides will be uploaded before each course day.
Book: Martinussen, Skovgaard, Sørensen: A first guide to statistical computations in R, Biofolia 2012, ISBN 978-87-913-1956-3. Your old textbook on introductory statistics (whatever that is) might also be usefull.
Zipped file with data for the book Guide1data.zip. Download and unzip the file to get a folder Guide1data containing the datasets from the book. To load a particular dataset from an R session you may use a command like load("beedata.rda"). If you are working in R from the directory that contains the Guide1data folder you have to write load("Guide1data/beedata.rda"). Use Session -> Set Working Directory from the top menu of RStudio to change the current Working Directory if necessary.

Session number	Date	Topic	Book pages	Details
1	November 18, 2020	Basic principles	Chapters 1, 3, and 4	link
2	November 25, 2020	Counts and proportions	Chapter 6 (possibly skipping 6.1 and 6.3)	link
3	December 2, 2020	Categorical regression	Chapter 10 (skipping 10.1.2 and 10.1.3)	link
4	December 9, 2020	Regression analysis + Analysis of Variance	Chapters 7	link
5	December 16, 2020	Random effects + Repeated measurements	Chapter 9 (skipping 9.4, 9.6 and 9.7)	link
6	January 6, 2021	Non-linear regression + Design of Experiments + Mediation and Confounding	Chapters 11	link

Details for each day of the course

Day 1: November 18, 2020

Link to online teaching (lectures)

Link to online teaching (exercise classes at 12:45)

Link to online teaching (exercise with TA / Phillip)

I suggest that you always start by using the first link for exercise classes when you log on at 12:45!

Slides

Exercise sheet

Exercises for Day 1
Exercise about ggplot2
Optional Exercise if you want to use the R Markdown format instead of just R scripts: rmarkdown.pdf

Data (from lectures and exercises)

Tenderness of pork meat (from Exercise 1.2): dataExample2.txt - dataExample2.xls
Phosphor concentration in lakes: lakes.xlsx
Hypertenstion in diabetic patients: hypertension.xls - hypertension.Rdata (RData - file)

R - programs (for lectures and some exercises)

Feeding concentrate and milk yield: feed_concentrate.R
Data example 1 from slides (Change in glucose level): glucose.R
Data example 3 from slides (Phosphor concentration in lakes): lakes.R
Part of the solution to Exercise 1.5: hint1_5.R

Day 2: November 25, 2020

Link to online teaching (lectures)

Link to online teaching (exercise classes at 12:45 by Bo Markussen)

Link to online teaching (exercise classes at 12:45 by Phillip)

LabApplStat R-package (by Bo Markussen)

Bo Markussen (who developed the teaching material for this course) has created an R-package LabApplStat that you are asked to install on your computer.

If you are using the latest version of R (4.0.3), and you have installed the devtools R-package on your computer, then you should be able to install LabApplStat directly from github by running

devtools::install_github("bomarkussen/LabApplStat",upgrade="never")

You may also save the following tar.gz-file and install the package by running

install.packages("myfolder/LabApplStat_1.4.0.tar.gz", repos = NULL, type = "source")

Slides

Papers

Sifting the evidence—what’s wrong with significance tests?: Sifting the evidence
Beyond Power Calculations: Assessing Type S (Sign) and Type M (Magnitude) Errors: Type S M error

Exercise sheet

Exercises for Day 2

Data (from lectures and exercises)

Eye-testing: vision.xlsx
Tenderness of pork meat (from Exercise 2.1): dataExample2.txt - dataExample2.xls
Dramanine as a remedy against seasickness (from Exercise 2.3): dramanine.txt
Discretization of continuous variables (from Exercise 2.7): Galton.txt

R - programs (for lectures and some exercises)

Density of nerve cells (Data example 2 from Day 1): cellDensity.R
Avadex given to mice: avadex.R
Activity of chicken: chicken.R
Solution to Exercise 2.5

Day 3: December 2, 2020 (NB: Change of program!)

Important:

Exercise classes on December 2, 2020 are cancelled. Lectures have been moved until afternoon (12:45) and you have to use the following link.

Slides

Exercise sheet

Exercises for Day 3

Data (from lectures and exercises)

Mortality of beetles (Data example 1 - to be used also for Exercise 3.1): beetle.txt - beetle_long.txt - beetle_verylong.txt
Risk of company default (Data example 2): Company_default.csv
Hypertension (Data example 3): hypertension.txt
Taste of cheese (Data example 4): cheese.txt
Number of greenflies on lettuce leaves (Data example 5): greenflies.txt
Data for Exercise 3.3: GLA.txt
Data for Exercise 3.4: walks.txt
Data for Exercise 3.5: particles.txt