Lectures

Introduction to OU Models

module 8
week 15
comparative analysis
phylogenetic trees
Ornstein Uhlenbeck
Brownian motion

Comparative analyses with Ornstein-Uhlenbeck models
Apr 27, 2023
Marguerite Butler

The ggtree-verse

module 7
week 13
phylogenetic trees
phylo
ggtree
treedata

Working with trees with tidytree and plotting with ggtree
Apr 25, 2023
Marguerite Butler

All about trees

module 7
week 13
phylogenetic trees
nexus
fasta
newick
beast
iqtree

Getting trees in to R and understanding their formats
Apr 18, 2023
Marguerite Butler

 

Setting Up for IQTREE2

module 7
week 13
iqtree2
phylogenetic inference
command line

Getting set up for phylogenetic inference using IQTREE2 on your local machine
Apr 13, 2023
Marguerite Butler

Phylogenetic Inference with IQTREE2

module 7
week 13
iqtree2
phylogenetic inference
command line
gene concordance
site concordance
gene tree
species tree

Maximum Likelihood phylogenetic tree inference and gene-tree species-tree concordance
Apr 13, 2023
Marguerite Butler

Procrustes Superimposition and Analyses

module 6
week 13
geometric morphometrics
GPA
procrustes superimposition
size
shape

A tour of analyses with geometric morphometric data
Apr 11, 2023
Marguerite Butler

 

Morphometrics Overview

module 6
week 12
control structures
if else
(do) while
programming

Some important considerations in a typical workflow
Apr 4, 2023
Marguerite Butler

Rodent lower jaw (mandible). Lateral view of a Nectomys squamipes mandible, showing the 10 landmarks used in this work. 1) Anterior edge of the incisive alveolus; 2) Most posterior point of the diastema; 3) Junction between the mandible and the m1 root; 4) Junction between the molar base and the coronoid process; 5) Most posterior point at the articular process; 6) Most anterior point in the angular notch; 7) Most posterior point at the angular process; 8) Angular process base; 9) Inner edge of the mandibular symphysis; 10) Posterior edge of the incisive alveolus

Intro to Geometric Morphometrics

module 6
week 12
control structures
if else
(do) while
programming

Getting started with morphometrics
Apr 4, 2023
Marguerite Butler

 

Measurement Error

module 6
week 12
control structures
if else
(do) while
programming

No measurements are perfect, so quantifying repeatability is important
Mar 30, 2023
Marguerite Butler

Intro to Morphometrics

module 6
week 11
control structures
if else
(do) while
programming

Getting started with some issues in morphometrics
Mar 30, 2023
Marguerite Butler

Program Flow

module 5
week 11
control structures
if else
(do) while
programming

Control the flow of your program using programming control statements
Mar 28, 2023
Marguerite Butler

 

Vectorization with Apply Functions

module 5
week 10
apply
lists
for loops
programming

Apply functions can help with vectorization and scaling up
Mar 23, 2023
Marguerite Butler

 

Lists and For-Loops

module 5
week 10
lists
for loops
programming

Donʻt get frustrated, learn a few simple rules about lists. Then you can massively scale.
Mar 23, 2023
Marguerite Butler

Writing your own functions

module 4
week 8
programming
functions
methods
scope

and all about functions in R
Mar 21, 2023
Marguerite Butler

Joining data with dplyr

module 3
week 7
tidyr
tidyverse
dplyr
tibble
pipe

Add
Mar 9, 2023
Marguerite Butler

 

Reshaping data with dplyr

module 4
week 8
tidyr
tidyverse
dplyr
tibble

Add
Mar 9, 2023
Marguerite Butler

A small review of univariate parametric statistics

module 3
week 8
univariate
statistics
ggplot2
dplyr

Add
Mar 7, 2023
Marguerite Butler

A small tour of multivariate analysis

module 3
week 7
multivariate
statistics
R

Add
Feb 28, 2023
Marguerite Butler

Getting data in shape with dplyr

module 3
week 7
tidyr
tidyverse
dplyr
tibble
pipe

Add
Feb 28, 2023
Marguerite Butler

The ggplot2 package

module 3
week 7
R
programming
plotting
ggplot2
data visualization

Introduction to the gplot2 grammar of graphics
Feb 21, 2023
Marguerite Butler

Plotting Systems

module 3
week 6
plotting
ggplot2
lattice
data visualization

Showing you base plotting, lattice, and ggplot2
Feb 16, 2023
Marguerite Butler

Tidying and Exploring Data

module 2
week 4
data
data structures
objects

All about data and how it is represented in R
Feb 14, 2023
Marguerite Butler

A cartoon showing two people arguing at a table, and a third person, the data analyst is at his laptop. He is smiling and says *When you two have finished arguing your opinions, I actually have data*.

Types of Data

module 2
week 4
data
data structures
objects

All about data and how it is represented in R
Feb 9, 2023
Marguerite Butler

 

Saving your work as R scripts

module 1
week 3
R
scripts
reproducibility

Add
Feb 7, 2023
Marguerite Butler

What is the question?

module 2
week 3
data
questions
data mining

Letʻs talk about scientific excellence & what data can and cannot do
Jan 31, 2023
Marguerite Butler

Data IO

module 2
week 3
data
input
output
formats

So many ways to get data into R
Jan 31, 2023
Marguerite Butler

 

Reference management

module 1
week 3
Quarto
authoring
BibTeX
programming

How to use citations and include your bibliography in R Quarto.
Jan 31, 2023
Marguerite Butler

Reproducible Research

module 1
week 2
R
reproducibility

Introduction to reproducible research
Jan 26, 2023
Marguerite Butler

Literate Statistical Programming and Quarto

module 1
week 2
Markdown
Quarto
programming

Introduction to literate statistical programming tools including Quarto Markdown
Jan 26, 2023
Marguerite Butler

Introduction to git/GitHub

module 1
week 2
programming
version control
git
GitHub

Version control is a game changer; or how I learned to love git/GitHub
Jan 24, 2023
Marguerite Butler

Introduction to your computerʻs terminal utilities

module 1
week 1
programming
filesystem
shell

So much power; or how I got my computer to do my bidding
Jan 19, 2023
Marguerite Butler

 

Introduction and The Big Idea

module 1
week 1
introduction

The big idea
Jan 17, 2023
Marguerite Butler
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