Jon Zelner jzelner

Social epidemiologist with a focus on infectious disease and computational methods at the University of Michigan School of Public Health

jzelner / Multinomial_Logit_HMM.py

Last active August 30, 2016 20:33

Example of time-varying HMM transition matrix

	import numpy as np

	#A simple observation series
	obs = np.array([0, 0, 1, 0, 0])

	#initial state occupation probabilities
	#(flat prior over state occupancies when t = 0)
	initProbs = np.ones(4)/4

	#These are the time-constant transition rates (with zeros

jzelner / render_post.R

Last active August 29, 2015 14:03

	#!/usr/bin/env Rscript

	input <- commandArgs(trailingOnly = TRUE)
	KnitPost <- function(input, base.url = "/") {
	require(knitr)
	opts_knit$set(base.url = base.url)
	fig.path <- paste0("../figs/", sub(".Rmd$", "", basename(input)), "/")
	opts_chunk$set(fig.path = fig.path)
	opts_chunk$set(fig.cap = "center")
	render_jekyll()

jzelner / render_post.sh

Last active August 29, 2015 14:03

	#!/bin/bash

	FILE="${1}"

	if [[ $# != 1 ]]; then
	echo "Usage: ./render_post.sh <file>"
	exit
	fi

	if [[ ! -f "${FILE}" ]]; then

jzelner / index.html

Created January 28, 2015 14:37

jzelner / starterpackages.R

Created April 19, 2016 16:59

	# ipak function: install and load multiple R packages.
	# check to see if packages are installed. Install them if they are not, then load them into the R session.

	ipak <- function(pkg){
	new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
	if (length(new.pkg))
	install.packages(new.pkg, dependencies = TRUE)
	sapply(pkg, require, character.only = TRUE)
	}