title: “HTML” author: “Chance” date: “2024-11-05” output: html_document: toc: true toc_float: True Theme: spacelab code_folding: hide —

This is a tutorial on how to use rmarkdown for

reproducable reasurch

Here we can type long passages or discriptions of our data without using the #symbol in our first example we will be using the toothgrow dataset. in this experiment guinea pigs were given different amount of vitemen c to see tooth growth

to run r code in markdown in markdown fikle we need to denote the section that is condodered r code we call these sections chunks

below is a chunk

toothdata <- ToothGrowth

head(toothdata)
##    len supp dose
## 1  4.2   VC  0.5
## 2 11.5   VC  0.5
## 3  7.3   VC  0.5
## 4  5.8   VC  0.5
## 5  6.4   VC  0.5
## 6 10.0   VC  0.5

as you can see from running the play button on the code chunk the results are printed inline of the rmarkdown file

fit <- lm(len ~ dose ,data = toothdata)

b <- fit$coefficients

plot(len ~ dose, data = toothdata)

abline(lm(len ~ dose, data = toothdata))
Figure 1: The tooth growth of Guinea pigs when given variable amounts of Vitamin C

Figure 1: The tooth growth of Guinea pigs when given variable amounts of Vitamin C

The slope of the regression line is 9.7635714

section headrs

we can put sections and sub sections in our r markdown file similar to numbers or bullet points in a word document this is done with # that we used to denote text in r script

first lvl header

second level header

third level header

make sure you put a space after the # otherwise it will not work

you can also you bullet point type marks in r markdown file - one item - one item - one item - one more item - one more item - one more item

it is important to note here that our markdown indentation matters

  1. First item
  2. second item
  3. third item - subitem 1 - subitem 2 - subitem 3

Block Quotes

we can put nice quotes into markdown document. we do this by using the > symbol > Genes are like the story and DNA is like the language that the story is written in. > > >— Sam Keen

formulas

we can also put nuce formated formulas into markdown using two doller signs

\[p^2 + 2pq + q^2 = 1\]

an dyou can get really complex

\[\theta = \begin{pmatrix\alpha} & beta\\ \gama & \delta \end(pmatrix}\]

Code Cunks

code chunk options

print("Hello world")

there are also options for r markdown file on how kniter interpurets the code chunk. there are the following options

eval (t or f ) wethir or not it evaluates the code chunk

echo (t or f) wether or not to show the code for the chunk but result will stay the same

cashe: if enable the same code chunk will not be evaluated the next time that the kinter is run great for code that has long run times

fig.width or fig.heiggt the (graphical device) size of the r plots in inches the figures are first written to the knitter document then to files that are saved seperate out.width or out.height- the output size of the rplots in the document.

fig.cap- the words for the figure captions

Table of contents

we can also add a table of contents to our HTML document by altering the YAML the weird code chunk at the top

Tabs

You can also add tabs in our report to do this you have to specify each section you want to be come a tab using this code “{.tabset}” after the line

Themes

You can also add theme to your HTML document that change the highting color and hyperlink color of your HTML can be nice astheticlly to do this you change your theme in the YAML to one of the following

cerulean journal flatly cosmo lumen paper simplex yeti null sandstone

code folding

you can use code folding for the reader to toggle between displaying the code and hiding the code this is done with:

code_folding: hide

These are a ton of ways to customize you r code with the HTML format this is also a great way to market yourself to interested parties.