1. Brief Intro to Knitr Package
What does Knitr do
R markdown file
More control over the output document
- Chunk options
- Global options
- Tables in knitr
- Knit vs. spin

2. What does Knitr do
Allows users to conduct reproducible research in R using Literate Programming
Versatility: any language as input(Python, Ruby, SAS, Scala…)
any markup language as output(Latex, Markdown, HTML…)
R Markdown
Create a R Markdown file with mixture of texts and codes
Process the R Markdown file through Knitr
final deliverables in form of Slides, PDF, HTML, etc. with evaluated R code output written inside
No more manually saving graphs as PNGs and pasting them to Doc file
Useful for reproducible reporting
knowledge of Latex or HTML is not necessary to make your reports look nice

3. R markdown file mixture of texts and codes exist in form of chunks
A R Markdown file example
some markdown syntax
R codes exist in R Markdown files in form of code chunk or inline code
Inline code:
The creation date of this report is `r Sys.Date()`
Code chunk:
```{r simulate_data}
x <- rnorm(100)
y <- 2*x + rnorm(100)
```
Render your .Rmd file

4. What would you like in your sandwich
Options
Chunk options
Echo = FALSE
results=“hide”
fig.width=8
fig.height=6
eval=TRUE
cache=FALSE
Global options
```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width=12, fig.height=8,
echo=FALSE, warning=FALSE, message=FALSE)
```

5. What would you like in your sandwich
Mathematical Notations
Equations can be formatted as inline notation or displayed formulas
inline equation : part of text
wrap by single $
$\sum_{i=1}^n X_i$
displayed formulas: displayed in a separate paragraph
wrap by a pair of $
$$\sum_{i=1}^n X_i$$
LATEX typesetting language can be directly inserted in R Markdown file to generate mathematical equation and notations
Some examples

6. What would you like in your sandwich
Tables in knitr
kable function in the knitr package
pandoc.table function in the pander package
xtable function in the xtable package

7. If you like what knit does for you ,
you might also want to checkout Spin
Generate draft .Rmd for you directly from R file
Using knit, your workflow might be:
With spin, your workflow looks like this:
Have your analysis ready in a R file
Create a Rmd file
copy and paste codes from R file into chunks in .Rmd
Render to knit
Have your analysis ready in a R file
Render to spin and get a draft .Rmd file
Add some markdown text and identify potential chunks in R file
Only need to add #+ before code to make it a chunk(instead of  ```{r} before the chunk and ``` after)
Still work as a normal R file so it’s easier to run codes cross chunks or source it

8. Reference R Markdown Cheat sheet knitr in a knutshell
Knitr documentaion by the author Yihui Xie