Chunks

Philippe Grosjean (phgrosjean@sciviews.org)

2020-04-16

The R package {knitr} is used to insert R code withing your Markdown document, which makes altogether an R Markdown document, usually with the .Rmd extension. Go to {knitr} homepage for more details. This document uses various chunks to see how they appears in a {pkgdown} site with the {svPkgdown} style.

R chunks

• A few R commands:

# This is a comment (don't use ##, since it is reserved for output!)
a <- 1 + 1 # Another comment
TRUE; NA; "Some text"

## [1] TRUE

## [1] NA

## [1] "Some text"

summary(cars) # A table

##      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

• Normal output versus message versus warning versus error:

# Normal output
cat("Some text...\n")

## Some text...

# A message
message("My very nice message")

## My very nice message

# Output with a warning
1:2 + 1:3

## Warning in 1:2 + 1:3: longer object length is not a multiple of shorter object
## length

## [1] 2 4 4

# An error
non_existing_object

## Error in eval(expr, envir, enclos): object 'non_existing_object' not found

• R chunk with option to generate a plot:

An example figure generated by R, from the cars dataset.

• Another plot:

library(ggplot2)
qplot(speed, dist, data = cars) + geom_smooth(method = "loess")

## Warning: `qplot()` was deprecated in ggplot2 3.4.0.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## `geom_smooth()` using formula = 'y ~ x'

Distance in function of speed for the cars data set.

Inline R expressions and special chunks

• Inline R expression like 2, or R version 4.4.1 (2024-06-14).

• Rcpp code chunks can also be included in your document:

#include <Rcpp.h>

// [[Rcpp::export]]
int fibonacci(const int x) {
    if (x == 0 || x == 1) return(x);
    return (fibonacci(x - 1)) + fibonacci(x - 2);
}

Because fibonacci() was defined with the Rcpp::export attribute it can now be called as a normal R function:

fibonacci(10L)

## [1] 55

fibonacci(20L)

## [1] 6765

• An R chunk that is displayed, but not executed:

library(knitr)
knit('R Markdown V2 Syntax.Rmd')