Building TeX file from knitr Rnw as child of larger parent TeX file to use R objects and output

Building TeX file from knitr Rnw as child of larger parent TeX file to use
R objects and output

Here's my general problem: I'm writing my dissertation using a LaTeX
template (http://www.latextemplates.com/template/masters-doctoral-thesis).
The template is a parent file with multiple chapters as children. For some
of the chapters, I want to include objects and output from R, whereas for
other chapters (e.g., Introduction) I don't want to use R. For the
chapters without R, I've created the .TeX files as part of the template.
Here's my specific problem: Right now I'm using knitr to create .TeX files
with R objects and output. I'm open to using other options (e.g., sweave)
if they'll work better for what I'm trying to do. I have some .TeX files
without R objects from a dissertation template that I want to combine with
.Rnw (or other) files with R objects. I want the .Rnw files to be created
as child .TeX files of the larger parent .TeX file. The parent-child
structure works for my .TeX files as part of the template using \input{}.
However, I'm having trouble getting the .TeX files created from the .Rnw
files to be included as child .TeX files. I've seen resources for
combining .Rnw files as child files of a larger parent .Rnw file (here),
but they appear to be combining only .Rnw files, not .Rnw files (with R)
with .TeX files (without R).
Because my template structure has a parent file, that's where I specify
the documentclass, begin document, etc. As a result, the child .TeX files
don't have headers. Thus, I first tried to create a .Rnw file without the
documentclass and begin document headers, but when I knit the .Rnw file
into .TeX and build the LaTeX files from all of the .TeX files, I receive
the following error:
! LaTeX Error: Environment knitrout undefined.
However, if I include the header in the .Rnw file with documentclass and
begin document, I receive the following error:
! LaTeX Error: Can be used only in preamble.
Below is the .Rnw file I'm using (with the header):
\documentclass{article}
\begin{document}
Here is a code chunk.
>=
1+1
letters
chartr('xie', 'XIE', c('xie yihui', 'Yihui Xie'))
par(mar=c(4, 4, .2, .2)); plot(rnorm(100))
@
You can also write inline expressions, e.g. $\pi=\Sexpr{pi}$, and
\Sexpr{1.598673e8} is a big number.
\end{document}
Below is the .TeX file generated from the .Rnw file:
\documentclass{article}\usepackage[]{graphicx}\usepackage[]{color}
%% maxwidth is the original width if it is less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the
margin)
\makeatletter
\def\maxwidth{ %
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\makeatother
\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
\def\at@end@of@kframe{}%
\ifinner\ifhmode%
\def\at@end@of@kframe{\end{minipage}}%
\begin{minipage}{\columnwidth}%
\fi\fi%
\def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
\colorbox{shadecolor}{##1}\hskip-\fboxsep
% There is no \\@totalrightmargin, so:
\hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
\MakeFramed {\advance\hsize-\width
\@totalleftmargin\z@ \linewidth\hsize
\@setminipage}}%
{\par\unskip\endMakeFramed%
\at@end@of@kframe}
\makeatother
\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
\usepackage{alltt}
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
Here is a code chunk.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969,
0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlnum{1} \hlopt{+} \hlnum{1}
\end{alltt}
\begin{verbatim}
## [1] 2
\end{verbatim}
\begin{alltt}
\hlstd{letters}
\end{alltt}
\begin{verbatim}
## [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q"
## [18] "r" "s" "t" "u" "v" "w" "x" "y" "z"
\end{verbatim}
\begin{alltt}
\hlkwd{chartr}\hlstd{(}\hlstr{"xie"}\hlstd{,} \hlstr{"XIE"}\hlstd{,}
\hlkwd{c}\hlstd{(}\hlstr{"xie yihui"}\hlstd{,} \hlstr{"Yihui
Xie"}\hlstd{))}
\end{alltt}
\begin{verbatim}
## [1] "XIE yIhuI" "YIhuI XIE"
\end{verbatim}
\begin{alltt}
\hlkwd{par}\hlstd{(}\hlkwc{mar} \hlstd{=}
\hlkwd{c}\hlstd{(}\hlnum{4}\hlstd{,} \hlnum{4}\hlstd{,}
\hlnum{0.2}\hlstd{,} \hlnum{0.2}\hlstd{))}
\hlkwd{plot}\hlstd{(}\hlkwd{rnorm}\hlstd{(}\hlnum{100}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/foo}
\end{knitrout}
You can also write inline expressions, e.g. $\pi=3.1416$, and
\ensuremath{1.5987\times 10^{8}} is a big number.
\end{document}
Thanks for your help in advance. FYI, I'm pretty new to LaTeX and
knitr/sweave.