| require(knitr) | |
| #' Initializes a new Gitbook. | |
| #' | |
| #' This will initalize a new Gitbook in the given directory. When done, it will | |
| #' also change the working directory. | |
| #' | |
| #' @author Jason Bryer <jason@bryer.org> | |
| newGitbook <- function(dir) { | |
| # TODO: May want to make these parameters or options |
The documents included are the input for knitr. In addition you need to have the tool pandoc installed. I also use a custom beamer template to add the University of Utah \institute command to the template. It also changes the indentation some.
| # Script name: instant_pkgs.R | |
| # Purpose: Package installation and loading | |
| # Author: Kay Cichini | |
| # Date: 2012-06-19 | |
| # Licence: cc by-nc-sa | |
| instant_pkgs <- function(pkgs) { | |
| pkgs_miss <- pkgs[which(!pkgs %in% installed.packages()[, 1])] | |
| if (length(pkgs_miss) > 0) { | |
| install.packages(pkgs_miss) |
| \documentclass[nohyper,justified]{tufte-handout} | |
| %\documentclass{article} | |
| %great guides at epslatex.pdf | |
| %check miniplot for potential use | |
| %\usepackage{graphics} | |
| %\usepackage{caption} | |
| %\usepackage{sidecap} | |
| %\usepackage{textpos} | |
| %\usepackage[section]{placeins} |
| Interactive charts and slides with R, googleVis and knitr | |
| ======================================== | |
| ```{r results='asis', echo=FALSE, message=FALSE, tidy=FALSE} | |
| library(googleVis) | |
| G <- gvisGeoChart(Exports, "Country", "Profit", | |
| options=list(width=250, height=120), chartid="c1") | |
| T <- gvisBarChart(Exports[,1:2], yvar="Profit", xvar="Country", | |
| options=list(width=250, height=260, | |
| legend='none'), chartid="c2") |
| \documentclass{article} | |
| %great guides at epslatex.pdf | |
| %check miniplot for potential use | |
| \usepackage{graphics} | |
| \usepackage{caption} | |
| %\usepackage{sidecap} | |
| %\usepackage{textpos} | |
| \usepackage[section]{placeins} |
| `r opts_chunk$set(cache=TRUE)` | |
| This is a quick set of analyses of the California Test Score dataset. The post was produced using R Markdown in RStudio 0.96. The main purpose of this post is to provide a case study of using R Markdown to prepare a quick reproducible report. It provides examples of using plots, output, in-line R code, and markdown. The post is designed to be read along side the R Markdown source code, which is available as a gist on github. | |
| <!-- more --> | |
| ### Preliminaries | |
| * This post builds on my earlier post which provided a guide for [Getting Started with R Markdown, knitr, and RStudio 0.96](jeromyanglim.blogspot.com/2012/05/getting-started-with-r-markdown-knitr.html) | |
| * The dataset analysed comes from the `AER` package which is an accompaniment to the book [Applied Econometrics with R](http://www.amazon.com/Applied-Econometrics-R-Use/dp/0387773169) written by [Christian Kleiber](http://wwz.unibas.ch/personen/profil/person/kleiber/) and [Achim Zeileis](http://eeecon.uibk.ac.at/~zeileis/ |
| This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) | |
| using [knitr](http://yihui.name/knitr/) in Rstudio 0.96. | |
| This combination of tools provides an exciting improvement in usability for | |
| [reproducible analysis](http://stats.stackexchange.com/a/15006/183). | |
| Specifically, this post | |
| (1) discusses getting started with R Markdown and `knitr` in Rstudio 0.96; | |
| (2) provides a basic example of producing console output and plots using R Markdown; | |
| (3) highlights several code chunk options such as caching and controlling how input and output is displayed; | |
| (4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and | |
| (5) discusses the implications of R Markdown. |
| library(ggplot2) | |
| library(colorRamps) | |
| IliganCity <- c(104493, 118778, 167358, 226568, 273004, 285061, 308046, 322821) | |
| CensalYear <- c("1970", "1975", "1980", "1990", "1995", "2000", "2007", "2010") | |
| qplot(CensalYear, IliganCity, xlab = expression(bold("Censal Year")), | |
| ylab = expression(bold("Population")), geom = "bar", colour = I("red"), | |
| fill = IliganCity, stat = "identity", ylim = c(0, 370000)) + theme_bw() + | |
| opts( |
| source('pubmed_trend.r') | |
| sex.pub <- pubmed_trend(search.str = 'Sex+Characteristics[mh] AND Pain[mh]', year.span=1970:2011) | |
| analgesic.pub <- pubmed_trend(search.str = 'Sex+Characteristics[mh] AND Analgesics[mh]', year.span=1970:2011) | |
| source('plot_bar.r') | |
| library("RColorBrewer") | |
| pdf(file='sex_pain.pdf', height=8, width=8) | |
| par(las=1) | |
| colorfunction = colorRampPalette(brewer.pal(9, "Reds")) |