The latex package "indentfirst" not working in R-markdown - latex

Question

I am trying to indent the first line after a section header using the indentfirst package but it is not working.
---
title: "Evaluation of Coaching Teachers by Program"
header-includes:
- \usepackage{indentfirst}
- \usepackage{booktabs}
- \usepackage{amsmath}
- \usepackage{pdflscape}
- \newcommand{\blandscape}{\begin{landscape}}
- \newcommand{\elandscape}{\end{landscape}}
author:
- "Office of Assessment and Accreditation"
- "University of South Carolina"
date: "August 2019"
output: pdf_document
---
\newpage
\blandscape
\section{\textbf{Introduction}}
The purpose of this report is to provide an overview.
\section{\textbf{Overview of all programs}}
\elandscape
Here is the latex output
\documentclass[]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\else % if luatex or xelatex
\ifxetex
\usepackage{mathspec}
\else
\usepackage{fontspec}
\fi
\defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\usepackage[margin=1in]{geometry}
\usepackage{hyperref}
\hypersetup{unicode=true,
pdftitle={Evaluation of Coaching Teachers by Program},
pdfauthor={Office of Assessment and Accreditation; University of South Carolina},
pdfborder={0 0 0},
breaklinks=true}
\urlstyle{same} % don't use monospace font for urls
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin#nat#width>\linewidth\linewidth\else\Gin#nat#width\fi}
\def\maxheight{\ifdim\Gin#nat#height>\textheight\textheight\else\Gin#nat#height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
%%% Use protect on footnotes to avoid problems with footnotes in titles
\let\rmarkdownfootnote\footnote%
\def\footnote{\protect\rmarkdownfootnote}
%%% Change title format to be more compact
\usepackage{titling}
% Create subtitle command for use in maketitle
\providecommand{\subtitle}[1]{
\posttitle{
\begin{center}\large#1\end{center}
}
}
\setlength{\droptitle}{-2em}
\title{Evaluation of Coaching Teachers by Program}
\pretitle{\vspace{\droptitle}\centering\huge}
\posttitle{\par}
\author{Office of Assessment and Accreditation \\ University of South Carolina}
\preauthor{\centering\large\emph}
\postauthor{\par}
\predate{\centering\large\emph}
\postdate{\par}
\date{August 2019}
\usepackage{indentfirst}
\usepackage{booktabs}
\usepackage{amsmath}
\usepackage{pdflscape}
\newcommand{\blandscape}{\begin{landscape}}
\newcommand{\elandscape}{\end{landscape}}
\begin{document}
\maketitle
\newpage
\blandscape
\section{\textbf{Introduction}}
The purpose of this report is to provide an overview of in
\section{\textbf{Overview of all programs}}
\elandscape
\end{document}
I want the first line after the section header to be indented.

Answer 1

The indentfirst package works, but something added \setlength{\parindent}{0pt} to your code, so the indention of the first paragraph is not visible because it is zero.
To revert this try with
\usepackage{indentfirst}
\setlength{\parindent}{20pt}
in your header includes.