What are the most important things to know about knitr R code chunk options for a beginner?

[jeromyanglim]

What are the most important things to know about knitr R code chunk options for a beginner?

[jeromyanglim]

Where to go to learn about knitr R code chunk options?

• http://yihui.name/knitr/options
• Rstudio also has code completion for knitr R code chunks

Give code chunks short informative names

Naming code chunks is optional but useful:

• increase code readability
• labels show up in R Studio navigation tools
• labels are used to create figure names and cached object names

The distinction between global and local R code chunk options?

Global options

LaTeX

 \Sexpr{ opts_chunk$set(opt = value) }

R Markdown

 `r opts_chunk$set(opt = value)`

I use global options particularly for:

• caching
• hiding console input for certain documents

Local options appear in code chunks.

The different delimiters for R Markdown and knitr LaTeX?

R Latex

<<insert_options_here>>=

@

R Markdown

```{r insert_options_here}

```

• Code options start with an optional name and a set of one or more options (also optional).
• All names and options are separated by a comma
• Each option is of the form option=value where option is a specified keyword, and value is an R expression, but typically a character, number, or TRUE/FALSE value.

How to hide console input?

echo = FALSE

How to hide unwanted output such as messages and errors?

warning=FALSE, error=FALSE, message=FALSE

How to hide console output?

results='hide'

How to output text that gets incorporated into output?

In LaTeX i often use cat to write raw tex output to create custom tables.
Similarly if you are using xtable to produce a HTML table, it is necessary for the output to be written literally to the document.

results='asis'

How to cache code chunks?

Often applied globally as

opts_chunk$set(cache=TRUE)

How to disable code tidying?

I often take care to arrange my code in a readable way and code tidying can reduce the readability.

tidy=FALSE

[piccolbo]

error=FALSE does something different, stops executions in case of error. I am still looking for a way to suppress errors while continuing execution.