Knitr/R Markdown: explore output controls

Some introductory test

In creating a vignette, these code & output display options are useful:

  1. no code display, no output
  2. display code, but not output
  3. display code with R prompt, but not output
  4. display code and output
  5. no code display, just the output
  6. tasteful display of a data.frame
  7. tasteful display of a data.frame, no ode
  8. show a previously created image

1. execute code: no code display, no output

{r label goes here, include=FALSE}

2. execute code, display code, no output

library(limma)

3. show R prompt, execute code, display code, no output

> library(limma)
> 2 + 1

4. display code and output

library(trenaSGM)
2 + 2

[1] 4

5. no code display, just the output

## [1] "variant 5"

6. tasteful display of a data.frame

knitr::kable(mtcars[1:5,], caption='mtcars')
mtcars
mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2

7. tasteful display of a data.frame, no code, no caption

mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2

8. show png image file

A quote:

Markdown is not LaTeX.

To compile me, run this in R:

library(knitr)
knit('001-minimal.Rmd')

See output here.

code chunks

A paragraph here. A code chunk below (remember the three backticks):

1+1
## [1] 2
.4-.7+.3 # what? it is not zero!
## [1] 5.551115e-17

graphics

It is easy.

plot(1:10)

hist(rnorm(1000))

inline code

Yes I know the value of pi is 3.1415927, and 2 times pi is 6.2831853.

math

Sigh. You cannot live without math equations. OK, here we go: \(\alpha+\beta=\gamma\). Note this is not supported by native markdown. You probably want to try RStudio, or at least the R package markdown, or the function knitr::knit2html().

nested code chunks

You can write code within other elements, e.g. a list

  1. foo is good

    strsplit('hello indented world', ' ')[[1]]
    ## [1] "hello"    "indented" "world"

  2. bar is better

Or inside blockquotes:

Here is a quote, followed by a code chunk:

x = 1:10
rev(x^2)
##  [1] 100  81  64  49  36  25  16   9   4   1

conclusion

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

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