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 via zoom TR 3:15-4:30
For more information email Dr. Blackmon.

Syllabus

Week	Topic	Material
1	Introduction and motivation	Class Survey PPT Slides PDF Slides Tuesday recording Thursday recording R script 1 HW 1 on Ecampus
2	Visualizing data	PPT Slides PDF Slides WS Chapter 2 plotting script Data file for homework 2 HW 2 on Ecampus Tuesday recording Thursday recording
3	Summaries and uncertainty	PPT Slides PDF Slides WS Chapter 1 and 3-4 HW 3 on Ecampus Tuesday recording Thursday recording
4	Probability and Discrete variables	PPT Slides PDF Slides WS Chapters 5-7 Tuesday recording Thursday recording script.R Chi-Sqaure test yates correction video bionimal test alternative agruments video
5	Winter Storm	No Classes
6	2 Continuous variables	PPT Slides PDF Slides script from lecture Tuesday video Thursday video crickets.csv
7	1 Continuous and 1 Discrete variable	PPT Slides PDF Slides Tuesday video Thursday video
8	GLM-1	PPT Slides PDF Slides WS Chapters 17 and 18 gnatocerus.csv oaks.csv chrysina.csv Tuesday video Thursday video
9	GLM-2	PPT Slides PDF Slides Tuesday video Thursday extra video midterm-review.pdf review script
10	Midterm	MIDTERM FILES Hardcopy of test vac.rates.csv mite.count.csv chicks.csv betta.csv
11	GWAS and ggplot	PPT Slides PDF Slides GWAS.R ggplot.R Thursday video
12	Comparative methods	PPT Slides PDF Slides Tuesday video tree data Thursday video
13	MCMC and Monte Carlo Methods	chiro.csv carn.csv Tuesday Video 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 Thursday Video
14	PCA	PCA PPT Slides PCA PDF Slides PCA .Rmd file PCA html file Tuesday Video Thursday Video
15	Project	Instructions and data for final project google drive for submission review files review sheet grasshopper mcmc1 mcmc2 Tuesday Video Thursday Video
16	Final	Exam and final project must be turned in before 5:00 PM on May 4th test.frogs.csv test.log.csv test.dispersal.csv test.contact.maps.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