Markdown

---

• .Rmd is Rstudio’s special blend of Markdown (a text rendering language)
• .md is the more generic Markdown file type. In RStudio, the intermediate .md files are not (in the default state) preserved.

Languages

• LaTeX Typesetting language invented in the 1970s by computer programmer Donald Knuth for proper rendering of text and equations. Hundreds of commands. Precise, but somewhat complicated to use.
• Markdown Greatly simplified version of LaTeX with a small number of commands to master. Easy to use, text looks great.
• yaml¹. Header material for .Rmd files that can be changed manually or by selecting options.
• R Computer language for manipulating numbers, text, graphics, statistics.

Using R-markdown

• pull up cheatsheet
• new .Rmd file

Basic text formatting

• headers # to ###### *numbering from options
• text
• markup
  • italic *<text>*
  • bold-face **<text>**
  • subscript ~<text>~
  • superscript ^<text>^
  • strikethrough ~~<text>~~
  • quotations >text with no closing mark

Spacing, manual breaks, lines

• line spacing effects
• two extra spaces at the end of a line for a manual break
• lists
  • indented
  • numbered

Links

• links [linking text](website address)
• footnotes²
• images

![image link](website address)

Tables

First Header  | Second Header
------------- | -------------
Content Cell  | Content Cell
Content Cell  | Content Cell

• also the kable package for later

{r, echo=TRUE,results='asis'}
library(knitr)
kable(head(iris))

library(knitr)
kable(head(iris))

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa
5.4	3.9	1.7	0.4	setosa

Fencing

• in line fencing to shade
• in line R code for calculations 6.1415927
• simple fencing to set off large chunks of plain text

Links

• links linking text
• footnotes³
• images

![image link](website address)

Tables

First Header  | Second Header
------------- | -------------
Content Cell  | Content Cell
Content Cell  | Content Cell

• also the kable package for later

{r, echo=TRUE,results='asis'}
library(knitr)
kable(head(iris))

library(knitr)
kable(head(iris))

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa
5.4	3.9	1.7	0.4	setosa

Equations

• in-line $

• centered $$

• basic math and text spacing handled by LateX

$$y = a + b$$

\[y = a + b\]

Subcripts

$$H_0 = Z_{a + b}$$

\[H_0 = Z_{a + b}\]

Superscripts

$$S = cA^z$$

\[S = cA^z\]

• elements can be coupled and nested

\[S=cA^z_1 + z_{2 + x}\]

$$S=cA^z_1 + z_{2 + x}$$

Fractions and Greek Symbols

\[\alpha = \frac{\beta}{\delta + \gamma_x}\]

$$\alpha = \frac{\beta}{\delta + \gamma_x}$$

Summation signs

\[z = \sum_{i=1}^X{K}\]

$$z = \sum_{i=1}^X{K}$$

“Escaping” the  special character in LaTeX

Use \backslash

$$\backslash \alpha \le b \backslash$$

\[\backslash \alpha \le b \backslash\]

Rendering plain text in a LaTex Equation

\[P(Occurrence Of Species A) = Z\]

$$P(Occurrence Of Species A) = Z$$

\[P(\mbox{Occurrence Of Species A}) = Z\]

$$P(\mbox{Occurrence Of Species A}) = Z$$

R Code in Chunks

• CTRL-ALT-I inserts a new “chunk” of R code

# Use comments extensively in ALL of your coding!
Pred <- seq(1,10)     # make a vector of integers from 1 to 10
Res <- runif(10)      # generate 10 draws from a random uniform (0,1) distribution

# print the random numbers
print(Res)

##  [1] 0.2383757 0.4377084 0.5717281 0.6752646 0.2680563 0.6470778 0.3148969
##  [8] 0.6643741 0.0141859 0.5488485

# plot the graph
plot(x=Pred,y=Res,type="b")

Using chunk options echo and eval to control printing of code and output

plot(runif(50),cex=10*runif(50),col="goldenrod")

print(rnorm(n=10, mean=10, sd=2))

##  [1]  9.799092  7.905844  8.292692 10.982835  9.774276  9.724717 10.017520
##  [8]  9.563490 10.651323 11.543441

Writing R scripts

• new script
• code executes and prints in console
• graphs in output window
• CTRL - ENTER to run a single line of code
• CTRL - SHIFT - ENTER to source and echo the entire script
• CTRL - SHIFT - S to source entire script without echoing console output
• CTRL - SHIFT - C comment and un-comment selected lines of code
• code to illustrate:

# First comment to explain what this program is doing.
# Be expansive and describe it in great detail. This may seem trivial, but will become increasingly important as you create complex programs.
# Simple script to examine the distribution of the product of two uniform variables
# Make sure it is readable. Use complete sentences, not cryptic phrases.
# 6 September 2018
# NJG

# Preliminaries
library(ggplot2)
set.seed(100)
library(TeachingDemos) # use this to set the random number seed from a character string
char2seed("green tea")
char2seed("green tea",set=FALSE)

## [1] 7023541

#

# Global variables
nRep <- 10000

# Create or read in data
ranVar1 <- rnorm(nRep)
# print(ranVar1)
head(ranVar1)

## [1] -0.67595800  0.07142749 -0.13803318 -0.99300667 -1.17181879  0.51340840

tail(ranVar1)

## [1]  0.35209291 -0.11819204  0.57509922 -0.05122504 -1.98879289 -1.04776740

ranVar2 <- rnorm(nRep)


# visualize data
qplot(x=ranVar1)

## 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.

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

# create product vector
ranProd <- ranVar1*ranVar2
length(ranProd)

## [1] 10000

str(ranProd)

##  num [1:10000] -1.3151 0.0117 0.1435 2.2531 -0.9411 ...

head(ranProd)

## [1] -1.31510790  0.01168855  0.14346105  2.25309300 -0.94114160  0.13995337

# do other stuff..

Converting .R files to .html (creating an R notebook)

• use notebook script
• roxygen comments `#

Purling to strip and consolidate R chunks from a Markdown file

• commands executed from console

library(knitr)
purl("FileName.Rmd")

These commands will create a file FileName.R that has all of the R code and none of the markdown text. R comments are still retained.

Leave RStudio and Work in Typora

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1. Originally “Yet Another Markdown Language”, but more recently “YAML Ain’t no Markdown Language”, which is a self-referencing acronym↩︎

2. Footnoted text, consecutively at bottom of page↩︎

3. Footnoted text, consecutively at bottom of page↩︎