Getting correct section numbering for Appendix in a large document

Question

I'm writing a thesis which is an aggregate of separate articles. I have the source code for the articles and I'm using \include to include them in the main document of the thesis. So in my main.tex (thesis document), I have

\include{article1}
some pages in between the two articles
\include{article2}

The problem that I'm getting is with the Appendix sections. In article 1, I have at the end:

\appendix
\numberwithin{equation}{section}
\section{Coefficients}\label{sec:Coeffic}
\subsection{Good coefficients}
then comes the first line of appendix

This gives in article 1 (when compiled separately with the article class):

A. Coefficients

A.1. Good coefficients

and equation numbers in the Appendix A as (A.1), (A.2)

which is ok and what is expected.

When I put article 1 within main.tex, I use \include command. Also, I removed the document class for article 1 and put \chapter instead.

But when I compile main.tex (the thesis document), I get the appendix sections as:

.1 Coefficients

.1.1 Good coefficients

and the equation numbers in the appendix A as (.1.1), (.1.2) etc

My article 1 is treated as a chapter in the main thesis document (main.tex) and the title and section numbers, equation numbers are preceded by A in main.tex. This is what I want.

Maybe it would be ok to get the appendix in my main.tex as

A.A. Coefficients

A.A.1 Good coefficients

and the equation numbers in the Appendix as (A.A.1), (A.A.2) etc

to denote that it refers to appendix A of paper A. First A is for the first article and second A is for first appendix. How to get this?

Answer 1

Preliminary remark: If an article includes an appendix (which is numbered as section A, subsection A.1, ...), and the article as a whole becomes chapter 1 of a book, the appendix in fact becomes a "subappendix" (which should be numbered as section 1.A, subsection 1.A.1, ...).

The \appendix command is defined by the document class - basically, it resets the counter of the "top section" level (\chapter in book, \section in article) and switches to Alphabetic numbering. So an \appendix command that is part of an "included" file will produce wrong results - it will redefine chapters instead of sections and in the process interfere with the numbering of subsequent chapters.

Solution: Change the definition of \appendix as to produce the desired formatting of "subappendices". (This way, you don't have to change your "included" files.) Keep the redefinition inside a group in order to allow for (main) appendix chapters.

\documentclass{book}

\usepackage{amsmath}

\usepackage{filecontents}

\begin{filecontents}{article1}
\section{foo}

Some text.

\appendix
\numberwithin{equation}{section}

\section{Coefficients}

\subsection{Good coefficients}

The first line of the appendix to article1.

\begin{equation}
a^2 + b^2 = c^2
\end{equation}
\end{filecontents}

\begin{document}

\begingroup

\renewcommand{\appendix}{%
  \par
  \setcounter{section}{0}%
  \renewcommand{\thesection}{\thechapter.\Alph{section}}%
}

\chapter{Title of article1}

\input{article1}

\endgroup

\appendix

\chapter{Title of (main) appendix}

Some text.

\end{document}

P.S.: I'd rather use \input instead of \include - you probably don't want a page break after the chapter title.