RMarkdown
?RStudio -> File -> New File ->R Markdown (keep defaults, add title)
Prompt to start new RMarkdown document.
Header for RMarkdown document.
Text and code chunk.
code-type font
1. A numbered
1. List
1. Can be made
1. Like this
HTML Headers:
#Header 1
##Header 2
###Header 3
Delete default RMarkdown text (except global options)
# Add Some Notes
## Reflections on Markdown So Far
Markdown is **super** awesome, I'm *not* even joking.
Why I love `RMarkdown`:
1. It makes things reproducible
2. Easy to collaborate
3. It's fun!
Markdown is super awesome, I’m not even joking.
Why I love RMarkdown
:
Generate basic RMarkdown document.
[text to show](http://the-web-page.com)
![image caption](http://url/for/file)
F~2~
and super-script ( F2): F^2^
.$E=mc^2$
or formulas: \[y = \mu + \sum_{i=1}^p \beta_i x_i + \epsilon\] ($$y = \mu + \sum_{i=1}^p \beta_i x_i + \epsilon$$
).A main code chunk:
Code chunk example
Place R code between the sets of ticks. You may also give each code chunk a name, which can help you find errors:
Named code chunk example
Can create a new code chunk manually (with backticks) or short-cut: CTRL+ALT+i.
[Importing surveys dataset into RMarkdown and creating a visualization with R code chunk options.]
library(ggplot2)
library(dplyr)
download.file("http://kbroman.org/datacarp/portal_clean.csv", "portal_clean.csv")
surveys <- read.csv("portal_clean.csv")
ggplot(surveys, aes(x=weight, y=hindfoot_length)) +
geom_point(aes(color=species_id, shape=sex)) +
facet_wrap(~year)
Example of R code chunk options specifyin that the code should not be output in the final report (echo=FALSE) and any messaged should also be suppressed (message=FALSE)
echo=FALSE
: supress code from being printed in final reportresults="hide"
: avoid having any results printed.eval=FALSE
: do not evaulate the code in the chunk.warning=FALSE
and message=FALSE
hides any warnings or messages produced.fig.height
, fig.width
controls size of figures (in inches).fig.cap
: adds a caption to the figures.fig.path
: defines path where figures will be saved. Example: ..., fig.path="Figs/",...
Global code chunk example
Plot with chunk options example
Species weight and height by year
`r
and `
for an in-line code chunk.
`r round(some_value, 2)`
. The code will be executed and replaced with the value of the result.echo=FALSE
and results="hide"
(which is equivalent to include=FALSE
).surveys <- read.csv("portal_clean.csv")
There are `r nrow(surveys)` observations in the *surveys* dataset.
There are 30652 observations in the surveys dataset.
(May take some additional installation on your computer)
In addition to HTML documents, RMarkdown can also knit to PDF or Word documents.
Other output format options