Template

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

R Markdown - what is it?

R Markdown is just Markdown + R code. It is a formatting syntax.

knitr converts R Markdown (runs the code) –> Markdown –> html

Knitr in a knutshell - Karl Broman

Some of this is from K Broman’s knitr tutorial.

Chunks

x <- rnorm(100)
y <- 2*x + rnorm(100)
cor(x, y)
## [1] 0.9036892

Inline code

Here we can have R code in line such as:

We have 3 items. Also x[1] = -2.04.

Never hard code a result or summary statistic again!

Chunk Options

echo=FALSE        Don't include the code
results="hide"    Don't include the output 
include=FALSE     Don't show code or output
eval=FALSE        Don't evaluate the code at all
warning=FALSE     Don't show R warnings
message=FALSE     Don't show R messages 
fig.width=#       Width of figure
fig.height=#      Height of figure
fig.path="Figs/"  Path for figure files

Global chunk options

knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/',
                      echo=FALSE, warning=FALSE, message=FALSE)

Knitr compiles to .md

To compile me, run this in R:

library(knitr)
knit('intro-rmarkdown.Rmd')

conclusion (via Yihui Xie:)

Nothing fancy. You are ready to go. When you become picky, go to the knitr website.

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