Experimental Design

Learning Objective

This course is intended to provide a foundation in the proper design of scientific research projects in the field of biology.

By the end of the course, successful students will be able to:

Design studies that are statically tractable
Graphically explore data in R
Perform standard statistical analyses in the R environment

Class meets TR 11:10-12:25 in Butler 309
For more information email Dr. Blackmon.

Syllabus

Week	Topic	Material
1	Introduction and motivation	Class Survey PPT Slides PDF Slides R script 1
2	Visualizing data	PPT Slides PDF Slides WS Chapter 2 plotting script Data file for homework 2
3	Summaries and uncertainty	PPT Slides PDF Slides WS Chapter 1 and 3-4
4	Probability and Discrete variables	PPT Slides PDF Slides WS Chapters 5-7 Homework
5	2 Continuous variables	PPT Slides PDF Slides script from lecture
6	1 Continuous and 1 Discrete variable	PPT Slides PDF Slides orthoptera.csv
7	Plotting / review / midterm	midterm reveiw Files for midterm: vac.rates.csv mite.count.csv chicks.csv
8	ggplot2 / GLM-1	review midterm fundamentals of linear models PPT Slides PDF Slides gnatocerus.csv betta_splendens.csv google folder
9	GLM-2	PPT Slides PDF Slides stickleback.csv chrysina.csv
10	GWAS	PPT Slides PDF Slides
13	MCMC and Monte Carlo Methods	chiro.csv carn.csv MCMC pdf MCMC PDF walks you through what we did in class and is also an example of the kind of thing you can make with Rmarkdown MCMC PPT Slides MCMC PDF Slides retrogenes.csv MC PPT Slides MC PDF Slides
13	MCMC and Monte Carlo	GLM homework Monte Carlo homework genome.data.csv high-dnds.csv
14	Data Wrangling and Practice	coleo.mcmc.log catwalk.data.csv
15	Review and Shiny	review sheet gnatocerus.male.csv newt.repro.csv hiC.data.csv
16	Final	sword.csv test.log.csv

Exam files

Extra Resources

R markdown
R style guide
basics of R cheat sheet
base R plotting cheat sheet
ggplot2 cheat sheet
color brewer

Useful R packages

swirl
ggplot2
coda