Trevor Bedford trvrb

Scientist at the Fred Hutch, studying viruses, evolution and immunity. Maintains @blab, @nextstrain and @seattleflu.

trvrb / index.html

Created May 28, 2012 16:35

Layering maps and D3

	<!DOCTYPE html>
	<html>
	<head>
	<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js?1.29.5"></script>
	<script type="text/javascript" src="http://polymaps.org/polymaps.min.js?2.5.0"></script>
	<style type="text/css">

	@import url("http://polymaps.org/style.css");

	html, body {

trvrb / d3.js ~ Treemap.htm

Created July 20, 2012 14:27 — forked from jasondavies/d3.js ~ Treemap.htm

Testing layout.pack transitioning


	<!DOCTYPE html>
	<html>
	<head>
	<meta http-equiv="content-type" content="text/html;charset=utf-8">
	<title>d3.js ~ Treemap</title>
	<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js"></script>
	<style type="text/css">

	@import url("http://mbostock.github.com/d3/style.css?1.10.0");

trvrb / index.html

Created July 20, 2012 14:46

Testing layout.pack

	<!DOCTYPE html>
	<html>
	<head>
	<meta http-equiv="content-type" content="text/html;charset=utf-8">
	<title>d3.js ~ Treemap</title>
	<script type="text/javascript" src="http://d3js.org/d3.v2.js"></script>
	<style type="text/css">

	@import url("http://mbostock.github.com/d3/style.css?1.10.0");

trvrb / collect-nodes.rb

Created July 30, 2012 15:22

Ruby script to collate nodes and attributes from a BEAST MCC file

	#!/usr/bin/ruby

	# This script reads through an MCC tree and reads out tip attributes
	# Converting these to a more parsable tab-deliminated format
	# Relies on each label existing for every node

	# Load tree from file
	filename = ARGV[0]
	infile = File.new(filename, "r")
	tree = ""

trvrb / Rakefile

Last active December 14, 2015 08:19

Rakefile for LaTex. Collects all .tex in a directory and runs `pdflatex` and `bibtex` as necessary to produce complete PDFs.

	# Rakefile to collect all .tex files in a directory and run `pdflatex` and `bibtex` as needed to
	# produce PDF output. If a .tex file is updated `pdflatex -draftmode` will be run to produce new
	# .aux and .log files. These are used to determine whether `bibtex` needs to be run. If so `bibtex`
	# will always need to be followed by `pdflatex -draftmode`. With fully updated .aux and .bbl in
	# hand, a final `pdflatex` is run. The only hole in the logic I've found is that, when making a
	# small revision, this will run `pdflatex -draftmode` then `pdflatex` when only `pdflatex` is
	# required.
	#
	# Run `rake` to compile PDFs and `rake clean` to remove the intermediary cruft

trvrb / beast_checkpoint.rb

Last active December 15, 2015 14:49

Ruby script to restart BEAST runs. This constructs a new XML control file from the original control file and the last logged parameter values.

	#!/usr/bin/ruby

	# Designed to allow checkpointing of BEAST output files
	# Input: beast_analysis.xml output_file_1.log output_file_2.log ... tree_file.trees
	# Expect at least 3 files
	# This matches column names in log files to parameter names in the original XML to set initial conditions

	xml_filename = ARGV.shift
	tree_filename = ARGV.pop
	log_filenames = ARGV

trvrb / graph.json

Last active June 13, 2017 23:51

Network of Bedford lab projects

	{
	"nodes": [
	{
	"id": "Alli",
	"type": "member",
	"img": "http://bedford.io/images/team/allison-black.jpg"
	},
	{
	"id": "Sidney",
	"type": "member",

trvrb / d3-multichord.js

Last active January 3, 2018 00:11

VEG Network

	(function (global, factory) {
	typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('d3-array'), require('d3-path')) :
	typeof define === 'function' && define.amd ? define(['exports', 'd3-array', 'd3-path'], factory) :
	(factory((global.d3 = global.d3 \|\| {}),global.d3,global.d3));
	}(this, function (exports,d3Array,d3Path) { 'use strict';

	var cos = Math.cos;
	var sin = Math.sin;
	var pi = Math.PI;
	var halfPi = pi / 2;

trvrb / .block

Last active July 29, 2019 05:50 — forked from mbostock/.block

Arc Tween

license: gpl-3.0

trvrb / ceirr-data.json

Last active February 21, 2020 01:52

CEIRR Network