Basic Skills in R Markdown

The HTML file (October, 2021)

1 Introduction

This document provides basic tools to produce a html file using R markdown. The best way to use this document is to run the file in R studio and then read the .Rmd file to see how the output was created. The file can be used to produce a very basic html document an you can add later more components to you document.

2 Sections and subsections

This is a an example of a R markdown file that produces htnl output. This is a section in the document.

2.1 Subsection

This text apears in a subsection

2.1.1 Subsubsection

This text is a part of a subsection.

3 Including R code

3.1 Print R code and output

This is an example how to include R code and output in the document. We use the airquality data as an example.

x<-na.omit(airquality$Ozone)
print(x)

##   [1]  41  36  12  18  28  23  19   8   7  16  11  14  18  14  34   6  30  11   1  11   4  32  23
##  [24]  45 115  37  29  71  39  23  21  37  20  12  13 135  49  32  64  40  77  97  97  85  10  27
##  [47]   7  48  35  61  79  63  16  80 108  20  52  82  50  64  59  39   9  16  78  35  66 122  89
##  [70] 110  44  28  65  22  59  23  31  44  21   9  45 168  73  76 118  84  85  96  78  73  91  47
##  [93]  32  20  23  21  24  44  21  28   9  13  46  18  13  24  16  13  23  36   7  14  30  14  18
## [116]  20
## attr(,"na.action")
##  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54  55  56  57  58  59
## [25]  60  61  65  72  75  83  84 102 103 107 115 119 150
## attr(,"class")
## [1] "omit"

3.2 Do not print the R code but print the output

If we do not want to print the R code, but we want to see the output use the option echo=FALSE:

##   [1]  41  36  12  18  28  23  19   8   7  16  11  14  18  14  34   6  30  11   1  11   4  32  23
##  [24]  45 115  37  29  71  39  23  21  37  20  12  13 135  49  32  64  40  77  97  97  85  10  27
##  [47]   7  48  35  61  79  63  16  80 108  20  52  82  50  64  59  39   9  16  78  35  66 122  89
##  [70] 110  44  28  65  22  59  23  31  44  21   9  45 168  73  76 118  84  85  96  78  73  91  47
##  [93]  32  20  23  21  24  44  21  28   9  13  46  18  13  24  16  13  23  36   7  14  30  14  18
## [116]  20
## attr(,"na.action")
##  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54  55  56  57  58  59
## [25]  60  61  65  72  75  83  84 102 103 107 115 119 150
## attr(,"class")
## [1] "omit"

4 Items

This is a text that contains items:

Item 1
Item 2
Item 3
Item 4

5 Use R as a part of your text

5.1 Example: summary statistics

The mean Ozone level is

x<-na.omit(airquality$Ozone)
mean(x)

## [1] 42.12931

with variance is equal to

var(x)

## [1] 1088.201

5.2 Graphical displays in the document

A histogram for the Ozone level can be produced using the function qplot with the option geom = “histogram”:

Ozone.R<-data.frame(x)
qplot(x, data = Ozone.R, geom = "histogram", binwidth = 0.1)

## 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.

To add a caption to the figure we use {r figchp1,fig.cap=“Sepal length (III)”}.

Ozone.R<-data.frame(x)
qplot(x, data = Ozone.R, geom = "histogram", binwidth = 0.1)

Figure 5.1: Sepal length (III)

We can refer to the figure from the text in the document. For example, Figure 5.2 presents a histogram that was produced using the function qplot() function.

Ozone.R<-data.frame(x)
qplot(x, data = Ozone.R, geom = "histogram", binwidth = 0.1)

Figure 5.2: Sepal length (III)

6 How to add a link to your document

Materials about R markdown are widely available online.

For a YouTube tutorial about R markdown by Jalayer Academy see YTRmd1.
For a second YouTube tutorial about R markdown by Roger Peng see YTRmd2.

A usefull link to a R Markdown:

For a free online book about R markdown see see RMDbook.

7 How to create a math formula

To create a math formula, for example a linear regression model of the form

\[y_{i}=\alpha+\beta \times x_{i} + \varepsilon_{i},\] we need to use \(LaTeX\) syntax.

8 Just do it

8.1 Analysis of the cars data

Fit a linear regression model to the cars datasets in which the response is the stopping distance and the predictor is the car speed.

8.2 Expected outout

Write a short report with the following structure

Introduction
The cars data (including a scapter plot of the data)
Modeling (formulate the model for the cars data)
Application to the data: present the results including the R object with the regression output. Plot os the data
and fitted model and isgnostic plots.

In your report, include the R code as a part of the text. Produce both html and pdf outputs.