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tree_size11 days ago
Tree Size | Simulating trees | Yule trees | Normalization by tree size | No normalization
Correlations1 months ago
Loading data
Getting started1 months ago
Using treestats | Multiple statistics
Speed improvement1 months ago
Speed | Timing the relationship with tree size | Worst culprits
Demonstrate isofemales1 months ago
Creation of isofemale lines
Demonstrate joyplot1 months ago
Demonstration of how to use joyplots
Empirical data1 months ago
Migration | Using simulation data as input | Mutation rate
Walkthrough1 months ago
GenomeAdmixR | Simulating an iso-female line | Visualizing individuals | Multiple source populations | Statistics | FST | LD | Selection
Visualization2 months ago
Plot over time | Plot Frequencies | plot difference frequencies | plot_start_end | joyplots | Plotting individual chromosomes
Overview_of_the_junctions_package4 months ago
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
Phased and unphased data4 months ago
Simulating data | Inferring the time since admixture | Population size | Simulating data with error
Junctions4 months ago
Junctions vignette | An infinite chromosome in a finite population | Including Random Markers | A Finite chromosome in a finite population | Other equations available
Walkthrough1 years ago
Guilds Vignette | The standard neutral model | Dispersal Guilds | Conditioning on Guild size | Guilds model with differences in dispersal
How to stretch an nLTT timepoints matrix4 years ago
Examples | Example: Easy tree | Example: Tree that has two branching events at the same time | Example: Complex tree
How to visualize nLTT values distributions4 years ago
Example: Easy trees | Example: Harder trees | Example: Five random trees
Walkthrough using the nLTT package4 years ago
nLTT statistic & nLTT plot | Average nLTT matrix & Average nLTT plot
nltt_diff functions4 years ago
Close to polytomies, easier to eyeball | Two pylogenies | Two LTT plots | Two nLTT plots
Trees with a root edge8 years ago
How to plot multiple nLTTs and their average9 years ago
Example: Easy trees | Example: Harder trees
Example workflow of STEPCAM10 years ago
What is STEPCAM | Required data | Starting STEPCAM
STEPCAM: plotting results10 years ago
Aim of this vignette | Data and STEPCAM