The combined three code chunks:

---
title: 'Your project title'
author: ''
date: ""
output:
  html_document:           # output document format
    toc: yes               # add table contents
    toc_float: yes         # toc_property: floating
    toc_depth: 4           # depth of TOC headings
    fig_width: 6           # global figure width
    fig_height: 4          # global figure height
    fig_caption: yes       # add figure caption
    number_sections: yes   # numbering section headings
    toc_collapsed: yes     # TOC subheading clapsing
    code_folding: hide     # folding/showing code 
    code_download: yes     # allow to download complete RMarkdown source code
    smooth_scroll: yes     # scrolling text of the document
    theme: lumen           # visual theme for HTML document only
    highlight: tango       # code syntax hightlighting styles
  pdf_document: 
    toc: yes
    toc_depth: 4
    fig_caption: yes
    number_sections: yes
  word_document:
    toc: yes
    toc_depth: '4'
---

```{css, echo = FALSE}
div#TOC li {     /* table of content  */
    list-style:upper-roman;
    background-image:none;
    background-repeat:none;
    background-position:0;
}

h1.title {    /* level 1 header of title  */
  font-size: 24px;
  font-weight: bold;
  color: DarkRed;
  text-align: center;
}

h4.author { /* Header 4 - and the author and data headers use this too  */
  font-size: 18px;
  font-weight: bold;
  font-family: "Times New Roman", Times, serif;
  color: DarkRed;
  text-align: center;
}

h4.date { /* Header 4 - and the author and data headers use this too  */
  font-size: 18px;
  font-weight: bold;
  font-family: "Times New Roman", Times, serif;
  color: DarkBlue;
  text-align: center;
}

h1 { /* Header 1 - and the author and data headers use this too  */
    font-size: 20px;
    font-weight: bold;
    font-family: "Times New Roman", Times, serif;
    color: darkred;
    text-align: center;
}

h2 { /* Header 2 - and the author and data headers use this too  */
    font-size: 18px;
    font-weight: bold;
    font-family: "Times New Roman", Times, serif;
    color: navy;
    text-align: left;
}

h3 { /* Header 3 - and the author and data headers use this too  */
    font-size: 16px;
    font-weight: bold;
    font-family: "Times New Roman", Times, serif;
    color: navy;
    text-align: left;
}

h4 { /* Header 4 - and the author and data headers use this too  */
    font-size: 14px;
  font-weight: bold;
    font-family: "Times New Roman", Times, serif;
    color: darkred;
    text-align: left;
}

/* Add dots after numbered headers */
.header-section-number::after {
  content: ".";
}
```

```{r setup, include=FALSE}
# code chunk specifies whether the R code, warnings, and output 
# will be included in the output files.

if (!require("knitr")) {                      # use conditional statement to detect
   install.packages("knitr")                  # whether a package was installed in
   library(knitr)                             # your machine. If not, install it and
}                                             # load it to the working directory.
#
knitr::opts_chunk$set(echo = TRUE,            # include code chunk in the output file
                      warning = FALSE,        # sometimes, you code may produce warning messages,
                                              # you can choose to include the warning messages in
                                              # the output file. 
                      results = TRUE,         # you can also decide whether to include the output
                                              # in the output file.
                      message = FALSE,        # suppress messages 
                      comment = NA            # remove the default leading hash tags in the output
                      )   
```