Rmarkdown_tutorial.Rmd

---
title: "HTML"
author: "ozlemtuna"
date: "2024-08-09"
output: 
 html_document:
---

?rmarkdown::html_document

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.



### Linear regression analysis
#### Linear Model Creation: 
lm() is the function used to fit linear models in R.
dist ~ speed specifies the model formula, where dist is the dependent variable (response) and speed is the independent variable (predictor).
data = cars indicates that the data to be used is from the cars dataset, which is a built-in dataset in R containing data on the speed of cars and the corresponding stopping distances.
#### Extract Coefficients: 
coef(fit) extracts the coefficients from the fitted model fit.
The result b will contain two coefficients: the intercept and the slope of the regression line. 
b[1] is the intercept, and b[2] is the slope of the line.
#### Plot the Data:
plot(cars) creates a scatter plot of the cars dataset, with speed on the x-axis and dist on the y-axis.
This plot visualizes the relationship between car speed and stopping distance.
#### Add Regression Line:
abline(fit) adds the regression line to the existing plot.
This line represents the linear model that was fitted to the data, showing the best-fit line that minimizes the difference between observed and predicted stopping distances.


```{r}
fit = lm(dist ~ speed, data = cars) # lm() is the function used to fit linear models in R.
b = coef(fit) # coef(fit) extracts the coefficients from the fitted model fit.
plot(cars) # plot(cars) creates a scatter plot of the cars dataset, with speed on the x-axis and dist on the y-axis.
abline(fit) # abline(fit) adds the regression line to the existing plot.
```

#Create a content file in Rmarkdown;

title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
---

# HTML
This is a level 1 heading (H1) in your RMarkdown document. The `#` symbol indicates the highest level of heading. In the context of your document:

- **HTML** is the main section or chapter.
- In the output HTML file, this will be styled as a large, prominent heading.

## toc
This is a level 2 heading (H2). The `##` symbol creates a subheading under the main section. 

- **toc** stands for "table of contents." In this context, it usually refers to settings related to the table of contents in your document.
- The heading `toc` might be used to group settings or explanations related to the table of contents.

### toc_depth
This is a level 3 heading (H3). The `###` symbol creates a subheading under the `toc` section.

- **toc_depth** specifies how many levels of headings should be included in the table of contents. For example, setting `toc_depth: 2` will include only `#` and `##` level headings in the TOC.
- If you want all headings (from `#` to `####`) to appear in the TOC, you set `toc_depth: 4`.

#### toc_float
This is a level 4 heading (H4). The `####` symbol creates a subheading under the `toc_depth` section.

- **toc_float** is a setting that, when enabled, allows the table of contents to "float" or remain visible as you scroll down the document.
- Setting `toc_float: true` makes the TOC panel stay in view, which is useful for navigating long documents.

## toc: true : Create a content file
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
---

# toc_depth: 2 : For two subheadings in the table of contents;

---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    toc_depth: 2
---


# toc_float: true : To align the table of contents to the left; 
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    toc_depth: 2
    toc_float: true
---  

   
## toc_float collapsed: To hide subheadings;
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    toc_float:
     collapsed: true 
---
    
## toc_float smooth_scroll: 
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    toc_float:
     smooth_scroll: true 
---

## number_sections: true : To add section numbers;
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    number_section: true
---
   
# Adding tabs to subheadings: .tabset 

#HTML {.tabset}
##toc
###toc_depth
####toc_float
 
# :.tabset-fade 

#HTML {.tabset .tabset-fade }
##toc
###toc_depth
####toc_float

# pill :  .tabset-pills

#HTML {.tabset .tabset-fade  .tabset-pills}
##toc
###toc_depth
####toc_float
 
# Adding subheadings to the text:
---
title: "demo"
subtitle: "subdemo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    number_section: true
---

# Font styles

italic: _italic_ or *italic*
bold: __bold__ or **bold**
Subscript: H~2~O
Superscript: x^2^ 
code: `code`

# Linking 

## linking
[BMGLab](https://bmglab-ege.com)

##adding image
![BMGLabimage](https://bmglab-ege.com/static/media/bmglabold.1eed75cb6d4e9e176611.jpg)




# Writing Mathematical Equations

##Inline Equation Example:


$f(k) = {n\choose k} p^{k} (1-p)^{n-k}$

##Block Equation:

$$f(k) = {n\choose k} p^{k} (1-p)^{n-k}$$

# Creating R Code Snippets
```{r, chunk-label, results='hide',fig.height=4, fig.width=4}

```


#Commonly Used Option Definitions

eval: Evaluation of a code snippet

```{r}
do_it = Sys.Date() '2024-08-09'
```

```{r, eval= do_it}
x=rnorm(100)

```

# Commonly Used Option Definitions 

- `eval`: Determines whether the code chunk should be evaluated.
- `echo`: Decides whether the source code will be displayed in the output.
- `results`:
  - `'hide'`: Hides the output.
  - `'asis'`: Displays the output as it is.
- `collapse`: Decides whether to combine the text output and source code into a single code block in the output.
- `error`, `message`, `warning`: Controls whether to print errors, messages, or warnings.
- `include`: When set to FALSE for `echo`, `results`, `warning`, `message`, it means none of these options will be applied.
- `cache`: Determines whether unchanged chunks are rerun.
- `fig.height`, `fig.width`: Adjusts the size of the figure.
- `out.width`, `out.height`: Changes the percentage of the output's width and height.
- `fig.align`: Aligns the figure as 'left', 'center', or 'right' in the output.
- `fig.cap`: Adds a caption to the figure.
- `dev`: Used for saving R graphics.

```{r out.width = "20%"}
library(ggplot2)
ggplot(cars, aes(speed, dist)) + geom_point()
```

```{r out.width = "50%"}
ggplot(cars, aes(speed, dist)) + geom_point()
```

# Figures / Graphics

```{r}
plot(cars , pch = 18)
```

```{r, fig.show='hold', out.width='%50'}
par(mar = c(4,4,.2,.1))
plot(cars, pch=19)
plot(pressure,pch=17)
```

```{r,out.width='%25', fig.align='center',fig.cap='BMGLab'}
knitr::include_graphics('https://bmglab-ege.com/static/media/labgif.d195f52fc41469846a01.gif')

```
# Creating Tables
```{r tables-mtcars}
knitr::kable(iris[1:5, ], caption = 'Flowers')
```



# Viewing Datasets

## (`paged`) Viewing: Divides tables into pages across rows and columns.

---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    number_section: true
    df_print: paged

---
```{r}
mtcars
```
```{r cols.print=3, rownames.print=3}
mtcars
```

## (`kable`) Viewing: To show all rows.
---
title: "demo"
author: "ozlemtuna"
date: "2024-08-10"
output:
  html_document:
    toc: true
    number_section: true
    df_print: kable
---

## Reactable package: 

install.packages("devtools")
devtools::install_github("glin/reactable")
library(reactable)

reactable(iris)