Tree Size | Simulating trees | Yule trees | Normalization by tree size | No normalization

Loading data

Using treestats | Multiple statistics

Speed | Timing the relationship with tree size | Worst culprits

Creation of isofemale lines

Demonstration of how to use joyplots

Migration | Using simulation data as input | Mutation rate

GenomeAdmixR | Simulating an iso-female line | Visualizing individuals | Multiple source populations | Statistics | FST | LD | Selection

Plot over time | Plot Frequencies | plot difference frequencies | plot_start_end | joyplots | Plotting individual chromosomes

title: "Overview_of_the_junctions_package"author: "Thijs Janzen"date: "5/6/2021"output: rmarkdown::html_vignettevignette: >%\VignetteIndexEntry | Overview of the junctions package | Simulation functions | Phased and unphased simulations | Mathematical simulations | Backcrossing | Inferring the time since admixture | Junction based methods | Local ancestry based methods | Likelihood functions | Expected number of junctions | Mathematical expressions

Simulating data | Inferring the time since admixture | Population size | Simulating data with error

Junctions vignette | An infinite chromosome in a finite population | Including Random Markers | A Finite chromosome in a finite population | Other equations available

Guilds Vignette | The standard neutral model | Dispersal Guilds | Conditioning on Guild size | Guilds model with differences in dispersal

Examples | Example: Easy tree | Example: Tree that has two branching events at the same time | Example: Complex tree

Example: Easy trees | Example: Harder trees | Example: Five random trees

nLTT statistic & nLTT plot | Average nLTT matrix & Average nLTT plot

Close to polytomies, easier to eyeball | Two pylogenies | Two LTT plots | Two nLTT plots

Example: Easy trees | Example: Harder trees

What is STEPCAM | Required data | Starting STEPCAM

Aim of this vignette | Data and STEPCAM