Categories

All (27)

(do) while (1)

BibTeX (1)

Brownian motion (1)

GitHub (1)

Markdown (1)

Ornstein Uhlenbeck (1)

Quarto (2)

R (4)

apply (1)

authoring (1)

beast (1)

command line (2)

comparative analysis (1)

control structures (1)

data (3)

data structures (2)

data visualization (2)

dplyr (4)

fasta (1)

filesystem (1)

for loops (2)

formats (1)

functions (1)

gene concordance (1)

gene tree (1)

ggplot2 (4)

ggtree (1)

git (1)

if else (1)

input (1)

introduction (1)

iqtree (1)

iqtree2 (2)

lattice (1)

lists (2)

maps (1)

methods (1)

module 1 (7)

module 2 (3)

module 3 (4)

module 4 (4)

module 5 (3)

module 7 (4)

module 8 (2)

multivariate (1)

newick (1)

nexus (1)

objects (2)

output (1)

phylo (1)

phylogenetic inference (2)

phylogenetic trees (3)

pipe (2)

plotting (2)

programming (9)

reproducibility (2)

scope (1)

scripts (1)

sf (1)

shapefiles (1)

shell (1)

site concordance (1)

species tree (1)

statistics (2)

tibble (3)

tidyr (3)

tidyverse (3)

treedata (1)

univariate (1)

version control (1)

week 1 (2)

week 10 (2)

week 11 (1)

week 13 (4)

week 15 (2)

week 2 (3)

week 3 (2)

week 4 (2)

week 5 (2)

week 7 (4)

week 8 (3)

Lectures

Introduction to OU Models

module 8

week 15

comparative analysis

phylogenetic trees

Ornstein Uhlenbeck

Brownian motion

Comparative analyses with Ornstein-Uhlenbeck models

Marguerite Butler

Spatial Data

module 8

week 15

sf

shapefiles

ggplot2

maps

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

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

Marguerite Butler

The ggtree-verse

module 7

week 13

phylogenetic trees

phylo

ggtree

treedata

Working with trees with tidytree and plotting with ggtree

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

Marguerite Butler

Vectorization with Apply Functions

module 5

week 10

apply

lists

for loops

programming

Apply functions can help with vectorization and scaling up

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

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.

Marguerite Butler

Reshaping data with dplyr

module 4

week 8

tidyr

tidyverse

dplyr

tibble

Simple tools that really help get your data into the right shape

Marguerite Butler

Writing your own functions

module 4

week 8

programming

functions

methods

scope

and all about functions in R

Marguerite Butler

Joining data with dplyr

module 3

week 7

tidyr

tidyverse

dplyr

tibble

pipe

Combining datasets via merging or joining is a power tool

Marguerite Butler

A small tour of multivariate analysis

module 4

week 8

multivariate

statistics

R

When you have relationships among many variables or want to identify group structure

Marguerite Butler

A small review of univariate parametric statistics

module 4

week 7

univariate

statistics

ggplot2

dplyr

What regression and ANOVA mean when exploring data

Marguerite Butler

Getting data in shape with dplyr

module 3

week 7

tidyr

tidyverse

dplyr

tibble

pipe

Crack that whip!

Marguerite Butler

The ggplot2 package

module 3

week 7

R

programming

plotting

ggplot2

data visualization

Introduction to the gplot2 grammar of graphics

Marguerite Butler

Plotting Systems

module 3

week 5

plotting

ggplot2

lattice

data visualization

Showing you base plotting, lattice, and ggplot2

Marguerite Butler

Tidying and Exploring Data

module 2

week 5

data

data structures

objects

All about data and how it is represented in R

Marguerite Butler

Types of Data

module 2

week 4

data

data structures

objects

All about data and how it is represented in R

Marguerite Butler

Saving your work as R scripts

module 1

week 4

R

scripts

reproducibility

Save your hard work as scripts!

Marguerite Butler

Data IO

module 2

week 3

data

input

output

formats

So many ways to get data into R

Marguerite Butler

Reference management

module 1

week 3

Quarto

authoring

BibTeX

programming

How to use citations and include your bibliography in R Quarto.

Marguerite Butler

Literate Statistical Programming and Quarto

module 1

week 2

Markdown

Quarto

programming

Introduction to literate statistical programming tools including Quarto Markdown

Marguerite Butler

Reproducible Research

module 1

week 2

R

reproducibility

Introduction to reproducible research

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

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

Marguerite Butler

Introduction and The Big Idea

module 1

week 1

introduction

Marguerite Butler