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

5. no code display, just the output

## [1] "variant 5"

6. tasteful display of a data.frame

knitr::kable(mtcars[1:5,], caption='mtcars')

Table: 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.