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:
  1. Design studies that are statically tractable
  2. Graphically explore data in R
  3. 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