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 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