EVE109 FQ21
1
Introduction
1.1
Installing R and RStudio
1.2
Tour of RStudio
1.3
Installing packages
1.4
Basic functions in R
1.4.1
Exercise
: Write a script to find out what fraction of your life you’ve been at UC Davis
1.5
Classes
1.6
Vectors and dataframes
1.7
Subsetting
1.8
Plotting
1.8.1
Exercise
: Describe this plot in plain english. What conclusions can we draw?
1.9
Homework
1.9.1
Homework 1: Write a script that does the following:
2
Molecular Markers
2.1
Paths
2.2
Reading in data from spreadsheets
2.3
Simple capture recapture example
2.4
Homework
2.4.1
Homework 2: Write a script that does the following:
3
Genetic Diversity
3.1
Manipulating dataframes
3.2
Using the
adegenet
package to calulate heterozygosity
3.2.1
Plotting heterozygosity
3.3
Homework
3.3.1
Homework 3: Write a script that does the following:
4
Population Structure
4.1
The
aggregate
and
apply
functions
4.2
Running a clustering analysis and deciding on a K value
4.3
The Q matrix
4.4
Plotting
4.5
Homework
4.5.1
Homework 4: Write a script that does the following:
5
Haplotype networks
5.1
Indexing
5.2
Using
table
to count across multiple columns
5.3
Creating a haplotype network
5.4
Homework
5.4.1
Homework 5: Write a script that does the following:
6
Project Time!
7
Speciation and Hybridization
7.1
Match
7.2
Dealing with missing data
7.3
Writing your own functions
7.4
Hybrid allele frequencies
7.5
Making a PCA
7.6
Homework
7.6.1
Homework 5: Write a script that does the following:
8
Veteran’s Day
9
Sex-biased gene flow
9.1
Multiple plots
9.2
Intro to this week’s data
9.3
Homework
9.3.1
Homework 8: Write a script that does the following:
Published with bookdown
EVE 109: Molecular Ecology
Week 8
Veteran’s Day
No discussion this week!