Discover tgvaughan/R0-manuscript-materials Open Source project

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Created about 4 years ago
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tgvaughan

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Supplemental files and data for the manuscript "Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".

sicm

Unofficial HTML version of Sussman and Wisdom's "Structure and Interpretation of Classical Mechanics"

HTML

PirateScope

wxPython oscilloscope client for dangerousprototypes.com's Bus Pirate.

Python

icytree

Browser-based utility for phylogenetic tree visualisation.

JavaScript

MultiTypeTree

BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.

Java

MASTER

A versatile simulation engine for stochastic population dynamics models.

Java

bacter

Bacterial phylogenetics in BEAST 2.

Java

feast

Tasty additions to BEAST 2

Java

BDMM-Prime

Multi-type birth-death-sampling modelling for BEAST 2.

Java

BuildRoster

Employee roster generator.

Python

TimeTrees.jl

Phylogenetic tree type for julia

Julia

JsonBrowse

Basic graphical JSON object heirarchy browser

Java

remaster

High-fidelity stochastic tree simulation for BEAST 2.

Java

bioinf702_lectures

Lecture slides for bioinf702

HTML

BayesianMCMCLectures

Lectures I gave for a Bayesian statistics minicourse at the University of Hohenheim.

JavaScript

dvtm

Fork of dvtm (http://www.brain-dump.org/projects/dvtm) that provides simple runtime configuration of key bindings and other basic options via an ini-like config file.

EpiInf

BEAST 2 package for performing inference on epidemiological parameters using the exact likelihood.

Jupyter Notebook

h5shell

Command shell interface for HDF5 scientific data files.

Python

talks

Repository for my web-based talks

HTML

HamiltonianTreeDynamics

Rough visualisation of classical mechanics in tree space

Processing

PhotoDist

Estimate distances from stereo photo pairs.

Java

mEpiLabWorkshop

One day BEAST 2 workshop delivered to mEpiLab

JavaScript

pitchfork

Bayesian phylogenetic inference under models supporting explicit polytomies.

Java

HK_2018_Slides

Lecture for C3BI workshop in HK, 2018

JavaScript

ModelSelection

BEAST 2 code for simple model selection.

Java

beast.m4

Some basic m4 macros for BEAST 2 XMLs

HK_2018_MiniProject

Instructions and data for student mini-project at the 2018 C3BI course on molecular phylogenetics.

Python

BSLoader

Easily load R scripts provided by BEAST 2 packages.

icylog

Browser-based BEAST log file analyzer.

JavaScript

TransmissionChainAnalyses

Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.

ceskykrumlov2018_lectures

Talks presented at the 2018 Workshop on Population and Speciation Genomics, Cesky Krumlov

JavaScript

tgvaughan/R0-manuscript-materials

tgvaughan

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