raffdoc’s gists

raffdoc / phylometa_fxn.R

Created August 18, 2011 08:07 — forked from sckott/phylometa_fxn.R

Conduct phylogenetic meta-analysis from R calling Phylometa - These are functions needed in the code in file phylometa_inR_run.R.

	#####################################################################
	# Created by Scott Chamberlain
	# Ecology and Evolutionary Biology Dept., Rice University
	# Houston, TX 77005, USA
	# [email protected]
	#####################################################################

	# Function to split confidence intervals, this function is required in the below functions
	CI_split <- function(a){
	dd<-c(gsub("\\(","",unlist(strsplit(a[5],","))[1]),gsub("\\)","",unlist(strsplit(a[5],","))[2]))

raffdoc / bowelCancer.Rnw

Created November 5, 2011 21:44 — forked from psychemedia/bowelCancer.Rnw

Sweave script documenting the production of a funnel plot

	\documentclass[a4paper]{article}
	\SweaveOpts{echo=FALSE, keep.source=TRUE}
	\usepackage{a4wide}
	\usepackage{color}
	\usepackage{hyperref}

	\begin{document}
	\section{Example of self-documenting data journalism notes}

	This is an example of using Sweave to combine code and output from the R statistical programming environment and the LaTeX document processing environment to generate a self-documenting script in which the actual code used to do stats and generate statistical graphics is displayed along the charts it directly produces.

raffdoc / SweaveXeLaTeXExample.Rnw

Created November 21, 2011 08:05 — forked from mages/SweaveXeLaTeXExample.Rnw

Sweave XeLaTeX Example

	%!TEX TS-program = xelatex
	%!TEX encoding = UTF-8 Unicode
	%% Copyright 2011 Markus Gesmann


	\documentclass[a4paper]{article}

	\usepackage[noae,nogin]{Sweave}
	\usepackage{tikz}
	%% attachfile2 is patched to work with xelatex

raffdoc / knitr performance.r

Created April 12, 2012 20:51 — forked from timelyportfolio/knitr performance.r

	## title:First Attempt at a knitr Performance Report
	## author:Timely Portfolio

	require(PerformanceAnalytics)
	require(xtable)

	data(edhec)
	table.CalendarReturns(edhec[,1:3])[13:15]
	charts.PerformanceSummary(edhec[,1:3],
	colorset=c("gray50","steelblue2","steelblue4"),

raffdoc / performance summary.r

Created April 14, 2012 09:40 — forked from timelyportfolio/performance summary.r

performance summary RNW and R

	require(knitr)
	knit2pdf("performance summary.rnw")

raffdoc / ling-plot.Rnw

Created April 15, 2012 08:35 — forked from JoFrhwld/ling-plot.Rnw

A knitr source file for including linguistic notation as graphical elements in ggplot2


	\documentclass{beamer}
	\usetheme{Singapore}
	\usepackage{tipa}

	%% Make the r-code small
	\ifdefined\knitrout
	\renewenvironment{knitrout}{\begin{footnotesize}}{\end{footnotesize}}
	\else
	\fi

raffdoc / margintale_blog_2.R

Created April 15, 2012 20:15 — forked from theHausdorffMetric/margintale_blog_2.R

Time Series Heatmaps in ggplot2

	require(quantmod)
	require(ggplot2)
	require(reshape2)
	require(plyr)
	require(scales)

	# Download some Data, e.g. the CBOE VIX
	getSymbols("^VIX",src="yahoo")

	# Make a dataframe

raffdoc / knitR Performance Attempt 2.rnw

Created April 19, 2012 05:10 — forked from timelyportfolio/knitR Performance Attempt 2.rnw

	%% LyX 2.0.2 created this file. For more info, see http://www.lyx.org/.
	%% Do not edit unless you really know what you are doing.
	\documentclass[english,nohyper,noae]{tufte-handout}
	\usepackage{helvet}
	\usepackage[T1]{fontenc}
	\usepackage[latin9]{inputenc}
	\usepackage{babel}
	\usepackage[unicode=true,pdfusetitle,
	bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=1,
	breaklinks=true,pdfborder={0 0 0},backref=false,colorlinks=false]

raffdoc / knitR Performance Attempt 2.rnw

Created April 19, 2012 19:43 — forked from timelyportfolio/knitR Performance Attempt 2.rnw

	%% LyX 2.0.2 created this file. For more info, see http://www.lyx.org/.
	%% Do not edit unless you really know what you are doing.
	\documentclass[english,nohyper,noae]{tufte-handout}
	\usepackage{helvet}
	\usepackage[T1]{fontenc}
	\usepackage[latin9]{inputenc}
	\usepackage{babel}
	\usepackage[unicode=true,pdfusetitle,
	bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=1,
	breaklinks=true,pdfborder={0 0 0},backref=false,colorlinks=false]

raffdoc / ggplot2Cheat.r

Created April 27, 2012 05:41 — forked from jbryer/ggplot2Cheat.r

Graphic Parameters (symbols, line types, and colors) for ggplot2

	require(ggplot2)
	require(grid)

	theme_update(panel.background=theme_blank(),
	panel.grid.major=theme_blank(),
	panel.border=theme_blank())

	#Borrowed (i.e. stollen) from http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.R
	getColorHexAndDecimal <- function(color) {
	if(is.na(color)) {

Rafik Margaryan raffdoc