Michael Sachs sachsmc

sachsmc / CIbars.R

Created November 26, 2013 19:16

	cibars <- function(x, y, y.se, tinyfactor = 50, ...){

	lower <- y - 1.96*y.se
	upper <- y + 1.96*y.se

	segments(x0 = x, y0 = lower, x1 = x, y1 = upper, ...)
	tinybarwidth <- (max(x) - min(x))/tinyfactor

	segments(x0 = x - tinybarwidth, y0 = lower, x1 = x + tinybarwidth, y1 = lower, ...)
	segments(x0 = x - tinybarwidth, y0 = upper, x1 = x + tinybarwidth, y1 = upper, ...)

sachsmc / myBoxplot.R

Last active January 1, 2016 05:19

Boxplot with quantile whiskers



	myboxplot <- function(datalist, quantiles = c(.1, .9), names, ...){


	bp <- boxplot(datalist, plot = FALSE)

	quants <- sapply(datalist, function(df){

	quantile(df, quantiles, na.rm = T)

sachsmc / wald test for differences

Last active August 29, 2015 13:55

	favre <- function(model, coeff.index){

	favre2 <- matrix(c(1, -1, 0, 0,
	1, 0, -1, 0,
	1, 0, 0, -1
	), nrow = 3, ncol = 4, byrow = T)

	theta.hat <- favre2 %*% as.matrix(model$coeff[coeff.index])
	cov.hat <- favre2 %% vcov(model)[coeff.index, coeff.index] %% t(favre2)

sachsmc / ddplyWithTotals.R

Created February 5, 2014 02:24

ddplyWithTotals.R


	##############################################################
	## Author: Michael Sachs, [email protected]
	## Version 1.0
	## Date Updated: 9/16/2013

	# Description: An extension of the ddply function from the
	# plyr package that additionally evaluates the user-supplied
	# function on subsets defined by lower-order combinations of the
	# variables. This is useful for calculating sub-totals and totals.

sachsmc / freq-approach.R

Created August 20, 2014 14:28

frequentist approach

	## frequentist approach for comparison

	freq_leaveout <- function(formula) {

	leftout <- sapply(1:n.trials, function(i){

	fit.biv <- lm(formula, data = hat.test[-i, ])
	predict(fit.biv, newdata = hat.test)[i]

	})

sachsmc / Rjobs

Last active August 29, 2015 14:09

Parallel Jobs on Biowulf

	Rscript --vanilla run.R 1 > run-1.Rout
	Rscript --vanilla run.R 2 > run-2.Rout
	Rscript --vanilla run.R 3 > run-3.Rout
	Rscript --vanilla run.R 4 > run-4.Rout
	Rscript --vanilla run.R 5 > run-5.Rout
	Rscript --vanilla run.R 6 > run-6.Rout
	Rscript --vanilla run.R 7 > run-7.Rout
	Rscript --vanilla run.R 8 > run-8.Rout
	Rscript --vanilla run.R 9 > run-9.Rout
	Rscript --vanilla run.R 10 > run-10.Rout

sachsmc / example.Rmd

Created November 14, 2014 18:13

Sparklificator in rmarkdown

	---
	title: "Sparklify"
	author: "Michael Sachs"
	date: "November 14, 2014"
	output:
	html_document:
	self_contained: false
	---
	<head>
	<script type="text/javascript" src="jquery-1.11.1.min.js"></script>

sachsmc / man-legend.R

Last active May 29, 2018 21:36

Add manual legend in ggplot2

	tm <- data.frame(Marker = sort(rep(letters[1:5], 10)), x = runif(50), y = runif(50))

	p1 + geom_line(data = tm, aes(linetype = Marker, x = x, y = y), alpha = 0) +
	scale_linetype(guide = guide_legend(override.aes = list(alpha = 1)), labels =
	c(expression(A[1]), expression(A[2]), expression(A[3]), expression(A[4]), expression(A[5]))) +
	theme(legend.position = c(.75, .25))

sachsmc / Submit to biowulf

Last active August 29, 2015 14:21

MPI Apply on Biowulf

qsub -v np=52 -l walltime=424:00:00, nodes=26 simRun.bat

sachsmc / .block

Last active February 17, 2016 18:21

Scrape your personal Capital Bikeshare Trip data

license: mit