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The problem can be seen in the screenshot ; enter image description here

Thesis.tex file (main tex file)

\documentclass[chaparabic,ggit,ms,12pt,oneandhalf]{metu}
\usepackage{appendix}
\usepackage{longtable}
\usepackage[pdftex]{hyperref}
\PassOptionsToPackage{greek,english}{babel}         % ADDITIONAL 27.12.2018
\usepackage{natbib}     % ADDITIONAL 24.12.2018
\usepackage[all]{hypcap}
\usepackage{todonotes}
\usepackage{graphicx}
%\graphicspath{ {./images/} }
\usepackage[figuresright]{rotating}
\usepackage{xy} 
\usepackage{booktabs}
\usepackage{pifont}
\usepackage{color}
\usepackage{listings}
\usepackage{pdfpages}
\usepackage{array}
\usepackage{algorithm}
\usepackage{algorithmic}
\usepackage{float}
\usepackage{caption}
\usepackage{lastpage}
\usepackage{afterpage}
\usepackage{lipsum}
\usepackage{adjustbox}
\usepackage{rotating}
\usepackage{enumerate}                      % ADDITIONAL 02.02.2019
% \usepackage[english,greek]{babel}         % ADDITIONAL 27.12.2018
% \usepackage{cite}
% \usepackage{graphicx}
\usepackage{amsmath,amssymb} % define this before the line numbering.
\makeatletter          % ADDITIONAL 16.03.2019
\newcommand{\leqnos}{\tagsleft@true\let\veqno\@@leqno}          % ADDITIONAL 16.03.2019
\newcommand{\reqnos}{\tagsleft@false\let\veqno\@@eqno}          % ADDITIONAL 16.03.2019
\reqnos        % ADDITIONAL 16.03.2019  
\makeatother          % ADDITIONAL 16.03.2019
% \usepackage{ruler}
\usepackage{color}
% \usepackage[utf8x]{inputenc}
% \usepackage{footnote}
% \makesavenoteenv{tabular}
% \makesavenoteenv{table}
\usepackage{apalike}        % ADDITIONAL 24.12.2018
\usepackage{lscape}         % ADDITIONAL 27.12.2018
\numberwithin{equation}{chapter}


\renewcommand{\sectionautorefname}{\S}
\renewcommand{\subsectionautorefname}{\S}

\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\newcommand\descitem[1]{\item{\bfseries #1}\\} % ADDITIONAL 27.12.2018

\captionsetup{belowskip=12pt,aboveskip=8pt}
\newcommand{\tab}{\hspace*{2em}}
\DeclareGraphicsExtensions{.pdf,.png,.jpg}
% \usepackage{amsmath}
\usepackage{siunitx}
\usepackage{textcomp}
\usepackage{subcaption}
\usepackage{tikz}
\usepackage{mathtools}
% \usepackage{rotating}
%\PassOptionsToPackage{figuresright}{rotating}
\DeclarePairedDelimiter\ceil{\lceil}{\rceil}
\DeclarePairedDelimiter\floor{\lfloor}{\rfloor}
\newcommand{\EA}[1]{\textcolor{red}{[EA: #1]}}

% Name and Surname
\author{}
% Thesis Title English and Turkish
\title{Evaluating Urban Growth Trends by Using SLEUTH Model: A case study in Adana}
\turkishtitle{KENTSEL BÜYÜME TRENDLERİNİN SLEUTH MODELİ İLE DEĞERLENDİRİLMESİ; ADANA’DA BİR VAKA ÇALIŞMASI}

\date{Jan 2018}

% prof : Prof. Dr.
% assocprof : Assoc. Prof. Dr.
% assistprof : Assist. Prof. Dr.
% dr : Dr.
%
% Director of Institute
\director[prof]{}
% Head of Department
\headofdept[prof]{}
%
% Supervisor : English and Turkish
\supervisor{}
% \turkishsupervisor{  } %if you will hard-code the academic title
%
% Affiliation of Supervisor in English and possibly in Turkish
\departmentofsupervisor{Civil Engineering, METU}
%\cosupervisor[dr]{Itır Önal Ertuğrul}
%\departmentofcosupervisor{Robotics Institute, Carnegie Mellon University}
%
% Committee Members
% In general members are sorted according to their academic titles
%
% Proffesors (1)
% Associate Professors (2)
% Assistant Professors (3)
% Other (4)
% 
% IMPORTANT:  All affiliatons should fit in a single line
% If affiliation line is broken into two lines you should shorten the affiliation by using 
% abbrevations or any other means
%
% First committee member should be the chair of examining committee
% Typically the chair is one of the highest ranked committee members
% Ask your supervisor if you are not sure
\committeememberi[assocprof]{}
\affiliationi{Geodetic and Geographic Information Technologies}
% Second committee member is always your supervisor
\committeememberii[assocprof]{}
\affiliationii{School of Land Registry and Cadastre}
% If you are an M.Sc. student and your Co-Supervisor is in your 
% examination committee, then third committee member is always your co-supervisor
%
% IMPORTANT: If you are Ph.D. student your co-supervisor can not be in your 
% examination committee.

% \def\@proftitlename{Prof. Dr.}\def\@tproftitlename{Prof. Dr.}
% \def\@assocproftitlename{Assoc. Prof. Dr.}\def\@tassocproftitlename{Doç. Dr.}
% \def\@assistproftitlename{Assist. Prof. Dr.}\def\@tassistproftitlename{Yrd. Doç. Dr.}
% \def\@drtitlename{Dr.}\def\@tdrtitlename{Dr.}

\committeememberiii[assistprof]{}
\affiliationiii{Department of Forest Engineering}
% Fourth committee member
\committeememberiv[prof]{}
\affiliationiv{Department of Civil Engineering}
% Fifth committee member
\committeememberv[assocprof]{}
\affiliationv{Department of City and Regional Planning}
%
% Keywords : English & Turkish, Comma seperated
\keywords{Urbanization, Urban growth modelling, SLEUTH, Supervised classification}
\anahtarklm{Kentleşme, Kentsel Büyüme Modeli, SLEUTH, Kontrollü Sınıflandırma}
%
% Abstract in English
%
\abstract{Sed sed lacus at lorem maximus sodales vitae nec mauris. Etiam     consequat neque nisi, vel sollicitudin enim auctor sed. Donec ac arcu feugiat, pulvinar nunc sed, vehicula erat. Cras pulvinar risus nec dolor faucibus ornare. Cras sapien est, scelerisque sed risus eu, efficitur maximus est. Proin dolor ipsum, bibendum sed neque nec, posuere interdum justo. Nullam scelerisque pretium ante ut hendrerit. Duis convallis neque vitae blandit convallis. Donec vulputate quis neque at rutrum. Aliquam tincidunt justo at nunc faucibus lobortis. Mauris et aliquet risus. Nam velit dolor, congue sit amet augue eu, luctus efficitur nibh. Maecenas dapibus convallis fringilla. Nullam ac pretium magna. Nullam nec venenatis risus. Suspendisse potenti.

Fusce malesuada lacus in metus interdum ultrices. Vestibulum vitae velit elementum, porta leo gravida, tempus velit. Praesent a risus non ligula hendrerit fringilla non ut sem. Mauris fermentum a nibh auctor tincidunt. Aenean nec lorem in neque ultricies venenatis. Nulla facilisi. Pellentesque fermentum elementum enim, vitae porta libero. Nam porta tristique leo, in vestibulum ligula ultricies nec. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Proin auctor nulla auctor euismod euismod. Etiam finibus turpis vitae turpis rhoncus euismod. Cras congue nisi quis massa aliquam ultricies. Mauris tristique sem ut semper dapibus.}
%
% Turkish Abstract
%
\oz{Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas scelerisque mi vitae turpis ornare bibendum. Sed sit amet facilisis sem. Nunc facilisis eros quam, vitae congue nunc tempus vitae. Fusce dignissim enim dolor, vitae sollicitudin dui maximus quis. Donec dignissim sagittis diam quis ullamcorper. Quisque eget tempus mauris. Curabitur nulla ligula, convallis sit amet mauris sit amet, blandit egestas tortor. Nam nec orci quis leo ultrices ultricies ut eu erat. Donec pharetra eleifend ipsum, a rhoncus ante convallis id. Nunc a lectus at lectus tincidunt sollicitudin. Morbi in elit et quam semper consectetur. Vivamus condimentum turpis at odio eleifend aliquet at vitae ex. Nunc magna lectus, faucibus in neque a, tincidunt auctor erat. Nulla sit amet aliquam neque. Donec tristique blandit commodo.

Suspendisse aliquet id odio ut sollicitudin. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Aliquam scelerisque volutpat volutpat. Proin at odio justo. Nunc placerat lectus ex, a dignissim nisl mattis id. Fusce sit amet risus facilisis, sagittis velit eget, tincidunt quam. Duis egestas mattis erat a pulvinar. Cras in fringilla nisi.

Integer mollis bibendum felis eu condimentum. Donec ut lacinia tortor. Integer accumsan mauris lectus, et tincidunt purus tempus vitae. Maecenas eleifend, velit in euismod dignissim, nisl lacus vestibulum arcu, vel porta quam lorem quis felis. Sed sit amet magna sodales, blandit risus id, eleifend libero. Suspendisse potenti. Nam gravida, enim vitae aliquam feugiat, lectus sem pellentesque nisl, nec ultricies urna elit at dui. Fusce vel aliquam nulla. Integer convallis nibh nec diam eleifend fringilla. Donec molestie egestas odio vitae dignissim. Duis facilisis, magna ut semper posuere, quam sapien auctor neque, a pulvinar purus velit sed nisl.} 
%
% Dedication 
\dedication{Dedication}
%
%
% Acknowledgements   
\acknowledgments{
I would like to express my sincere ….}
%
% End of Personal and Introductory Information
\raggedbottom
\begin{document}
% Preliminaries
\begin{preliminaries}
% If you are willing to use any custom stuff before Chapters, put it here
% Such as List of Abbreviations
% Check the abbreviations.tex for a template list of abbreviations

\input{abbreviations.tex}
% End of Preliminaries
\end{preliminaries}
%   
% Latex content Goes Here 
% 
%

\setlength{\parindent}{0em}
\setlength{\parskip}{10pt}

% You can add as many chapters
\input{chapters/chapter1.tex}
\input{chapters/chapter2.tex}
\input{chapters/chapter3.tex}
\input{chapters/chapter4.tex}
\input{chapters/chapter5.tex}
\input{chapters/chapter6.tex}


% \input{references.tex}

%
% References in Bibtex format goes into below indicated file with .bib extension
%\bibliography{thesis_references}
% You can use full name of authors, however most likely some of the Bibtex entries you will find, will use abbreviated first names
% If you don't want to correct each of them by hand, you can use abbreviated style for all of the references

%\bibliographystyle{abbrv}
\bibliographystyle{apalike}        
\bibliography{thesis}

% if you have more that one appendix, then use \appendices, otherwise use 
\appendix
\input{chapters/appendix.tex}
\end{document}

Appendix.tex file;

\appendix
\renewcommand{\thesubsection}{APPENDIX \Alph{subsection}}
\chapter*{APPENDICES}
\subsection{Confusion Matrices of Classified Satellite Imagery}
\label{appendix:confusionMatrices}
% the \\ insures the section title is centered below the phrase: AppendixA

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 2018 Imagery}
\label{table:2018ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
class       & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture & 97          & 2        & 0      & 1     & 0     & 100        \\ \hline
Bareland    & 9           & 89       & 1      & 1     & 0     & 100        \\ \hline
Forest      & 20          & 4        & 73     & 2     & 1     & 100        \\ \hline
Urban       & 3           & 2        & 4      & 91    & 0     & 100        \\ \hline
Water       & 0           & 3        & 2      & 2     & 93    & 100        \\ \hline
Column Total  & 129         & 100      & 80     & 97    & 94    & 500        \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 2016 Imagery}
\label{table:2016ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
class       & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture & 96          & 1         & 0      & 3     & 0     & 100        \\ \hline
Bareland    & 16          & 80        & 4      & 0     & 0     & 100        \\ \hline
Forest      & 27          & 5         & 54     & 11    & 3     & 100        \\ \hline
Urban       & 10          & 4         & 5      & 81    & 0     & 100        \\ \hline
Water       & 4           & 0         & 3      & 0     & 93    & 100        \\ \hline
Column Total  & 153         & 90        & 66     & 95    & 96    & 500        \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 2011 Imagery}
\label{table:2011ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
class       & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture & 76          & 10        & 13     & 1     & 0     & 100       \\ \hline
Bareland    & 9           & 85        & 6      & 0     & 0     & 100       \\ \hline
Forest      & 2           & 2         & 96     & 0     & 0     & 100       \\ \hline
Urban       & 1           & 2         & 3      & 94    & 0     & 100       \\ \hline
Water       & 1           & 0         & 0      & 0     & 99    & 100       \\ \hline
Column Total   & 89          & 99        & 118    & 95    & 99    & 500       \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 2006 Imagery}
\label{table:2006ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
class       & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture & 77          & 19        & 2      & 2     & 0     & 100       \\ \hline
Bareland    & 2           & 92        & 3      & 3     & 0     & 100       \\ \hline
Forest      & 3           & 1         & 96     & 0     & 0     & 100       \\ \hline
Urban       & 4           & 5         & 10     & 81    & 0     & 100       \\ \hline
Water       & 0           & 0         & 0      & 0     & 100   & 100       \\ \hline
Column Total   & 86          & 117       & 111    & 86    & 100   & 500       \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 2001 Imagery}
\label{table:2001ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
class       & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture & 80          & 17        & 1      & 2     & 0     & 100       \\ \hline
Bareland    & 0           & 93        & 6      & 1     & 0     & 100       \\ \hline
Forest      & 0           & 1         & 98     & 1     & 0     & 100       \\ \hline
Urban       & 0           & 0         & 5      & 95    & 0     & 100       \\ \hline
Water       & 0           & 0         & 0      & 0     & 100   & 100       \\ \hline
Column Total   & 80          & 111       & 110    & 99    & 100   & 500       \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Confusion Matrix of Classification Result of 1990 Imagery}
\label{table:1990ConfusionMatrix}
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
Class        & Agriculture & Bareland & Forest & Urban & Water & Row Total \\ \hline
Agriculture  & 90          & 7         & 2      & 1     & 0     & 100       \\ \hline
Bare land    & 0           & 91        & 2      & 7     & 0     & 100       \\ \hline
Forest       & 0           & 0         & 97     & 3     & 0     & 100       \\ \hline
Urban        & 10          & 0         & 6      & 84    & 0     & 100       \\ \hline
Water        & 0           & 0         & 0      & 0     & 100   & 100       \\ \hline
Column Total & 100         & 98        & 107    & 95    & 100   & 500       \\ \hline
\end{tabular}
\end{table}

\subsection{\\Overall Accuracy Assessment Tables of Satellite Imagery}
\label{appendix:overallAccuracyTables}
% the \\ insures the section title is centered below the phrase: Appendix B


\begin{table}[H]
\center
\caption{Overall Accuracy Report of 2018 Classification}
\label{table:2018OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
overall acc. & class       & producers acc & User’s accuracy \\ \hline
0.87         & agriculture & 0.75          & 0.97            \\ \hline
             & bareland    & 0.89          & 0.89            \\ \hline
Kappa        & forest      & 0.91          & 0.73            \\ \hline
0.86         & urban       & 0.94          & 0.91            \\ \hline
             & water       & 0.99          & 0.93            \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Overall Accuracy Report of 2016 Classification}
\label{table:2016OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
Overall Accuracy & Class Type  & Producer’s Accuracy & User’s Accuracy \\ \hline
0.81             & agriculture & 0.63         & 0.96            \\ \hline
                 & bare land   & 0.89         & 0.8             \\ \hline
Kappa            & forest      & 0.81         & 0.54            \\ \hline
0.76             & urban       & 0.85         & 0.81            \\ \hline
                 & water       & 0.97         & 0.93            \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Overall Accuracy Report of 2011 Classification}
\label{table:2011OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
overall acc. & class type  & producers accuracy & user’s accuracy \\ \hline
0.9          & agriculture & 0.85               & 0.76            \\ \hline
             & bare land   & 0.86               & 0.85            \\ \hline
             & forest      & 0.81               & 0.96            \\ \hline
kappa        & urban       & 0.99               & 0.94            \\ \hline
0.88         & water       & 1                  & 0.99            \\ \hline          
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Overall Accuracy Report of 2006 Classification}
\label{table:2006OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
overall acc. & Class Data  & producer’s accuracy & user’s accuracy \\ \hline
0.89         & agriculture & 0.90                & 0.77            \\ \hline
             & bareland    & 0.79                & 0.92            \\ \hline
kappa        & forest      & 0.86                & 0.96            \\ \hline
0.87         & urban       & 0.94                & 0.81            \\ \hline
             & water       & 1                   & 1               \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Overall Accuracy Report of 2001 Classification}
\label{table:2001OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
overall acc. & Class       & Producers Accuracy & User’s Accuracy \\ \hline
0.93         & agriculture & 1                  & 0.8             \\ \hline
             & bareland    & 0.84               & 0.93            \\ \hline
kappa        & forest      & 0.89               & 0.98            \\ \hline
0.92         & urban       & 0.96               & 0.95            \\ \hline
             & water       & 1                  & 1               \\ \hline
\end{tabular}
\end{table}

\begin{table}[H]
\center
\caption{Overall Accuracy Report of 1990 Classification}
\label{table:1990OverallAccuracy}
\begin{tabular}{|c|c|c|c|}
\hline
Overall Accuracy &             & Producers Accuracy & Accuracy \\ \hline
0.92             & agriculture & 0.9                & 0.9      \\ \hline
                 & bareland    & 0.93               & 0.91     \\ \hline
kappa            & forest      & 0.91               & 0.97     \\ \hline
0.91             & urban       & 0.88               & 0.84     \\ \hline
                 & water       & 1                  & 1        \\ \hline
\end{tabular}
\end{table}

\subsection{\\Road Aggregation Schema}
\label{appendix:roadAggregationSchema}

\begin{figure}[H]
\centering
\includegraphics[width=0.3\columnwidth]{figures/roadClassification.jpg}
\captionsetup{justification=centering}
\caption{Aggregation Schema of Roads}
\label{fig:roadClassification}
\end{figure}

\subsection{\\Scenario Files}
\label{appendix:scenarioFiles}

\begin{landscape}
\begin{figure}[!htp]
\centering
\includegraphics[width=0.8\columnwidth]{figures/scenario1.png}
\captionsetup{justification=centering}
\caption{First Scenario File}
\label{fig:scenario1}
\end{figure}
\end{landscape}

\begin{landscape}
\begin{figure}[!htp]
\centering
\includegraphics[width=0.8\columnwidth]{figures/scenario2.png}
\captionsetup{justification=centering}
\caption{Second Scenario File}
\label{fig:scenario2}
\end{figure}
\end{landscape}

\begin{landscape}
\begin{figure}[!htp]
\centering
\includegraphics[width=0.8\columnwidth]{figures/scenario3.png}
\captionsetup{justification=centering}
\caption{Third Scenario File}
\label{fig:scenario3}
\end{figure}
\end{landscape}

\subsection{Input File Names According to SLEUTH Naming Convetion}
\label{appendix:sleuthNamingCon}
\begin{figure}[!htp]
\centering
\includegraphics[width=0.3\columnwidth]{figures/sleuthNamingConvetion.JPG}
\captionsetup{justification=centering}
\caption{Reorganized Layer Names According to SLEUTH Naming Style}
\label{figure:sleuthNamingConvetion}
\end{figure}

\subsection{Calibration Coefficients (OSM) of Coarse, Fine and Final Calibration}

\label{appendix:osmCoarseCal}
\begin{figure}[H]
\centering
\includegraphics[width=0.6\columnwidth]{figures/osmCoarseCal.png}
\captionsetup{justification=centering}
\caption{Coarse Calibration Coefficients with Highest OSM Values}
\label{fig:osmCoarseCalFig}
\end{figure}

\label{appendix:osmFineCal}
\begin{figure}[H]
\centering
\includegraphics[width=0.6\columnwidth]{figures/osmFineCal.png}
\captionsetup{justification=centering}
\caption{Fine Calibration Coefficients with Highest OSM Values}
\label{fig:osmFineCalFig}
\end{figure}

\label{appendix:osmFinalCal}
\begin{figure}[H]
\centering
\includegraphics[width=0.6\columnwidth]{figures/osmFinalCal.png}
\captionsetup{justification=centering}
\caption{Final Calibration Coefficients with Highest OSM Values}
\label{fig:osmFinalCalFig}
\end{figure}

\subsection{2030 Predictions}
\label{appendix:2030prediction}
\begin{figure}[H]
\centering
\includegraphics[width=0.9\columnwidth,height = 0.5\textheight,keepaspectratio]{figures/2030prediction.png}
\captionsetup{justification=centering}
\caption{2030 Prediction Without 2020 Road Layer}
\label{fig:2030prediction}
\end{figure}
5
  • 1
    You have to provide an MWE, it is impossible to guess what causes the error. Probably, you have code in the heading that disturbs the alignment.
    – Sveinung
    Commented May 19, 2019 at 9:12
  • @Sveinung question updated!
    – Capan
    Commented May 19, 2019 at 10:45
  • 1
    Where can we find metu.cls? I could not find it on CTAN. Could you please also turn your code snippets nto a compilable minimal working example (MWE)? Currently the code contains quite a lot of lnies that are most likely not related to the problem. Additionally, your example relies on external files.
    – leandriis
    Commented May 19, 2019 at 11:04
  • 1
    What is the \\ in \subsection{\\Overall Accuracy Assessment Tables of Satellite Imagery} supposed to do?
    – leandriis
    Commented May 19, 2019 at 11:07
  • Hi @leandriis I'm not sure what *\* doing int \subsection{\\Overall Accuracy Assessment Tables of Satellite Imagery}. I've uploaded the cls file to cloud. You can find it on this link; justbeamit.com/tyv42
    – Capan
    Commented May 19, 2019 at 11:13

1 Answer 1

0

I reduced your files to an MWE by deleting all unnecessary code. I localised the bad ToC to be connected to the obscure redefinition of subsection in the appendix file.

WARNING! I describe a quick and dirty fix!

What you should do, is redefine the subsection in a correct way in the appendix (i.e. rewriting the original definition of subsection) and redefine the ToC to secure enough room for the word APPENDIX.

I managed to get the following table of content by ensure that every subsection (heading) in your appendix.tex had its \\. This is not the correct way to do it, but obviously your templates are written by people not very familiar with LaTeX.

Your main document reduced to an MWE:

main.tex

\documentclass[12pt]{report}
\usepackage{appendix}

\raggedbottom

\begin{document}

\tableofcontents

\setlength{\parindent}{0em}
\setlength{\parskip}{10pt}

% You can add as many chapters
\chapter{chapters/chapter1.tex}
\chapter{chapters/chapter2.tex}
\chapter{chapters/chapter3.tex}
\chapter{chapters/chapter4.tex}
\chapter{chapters/chapter5.tex}
\chapter{chapters/chapter6.tex}

\appendix
\input{appendix.tex}
\end{document}

appendix.tex

\renewcommand{\thesubsection}{APPENDIX \Alph{subsection}}
\chapter*{APPENDICES}
\subsection{\\Confusion Matrices of Classified Satellite Imagery}

\subsection[\\Confusion Matrices]{Overall Accuracy Assessment Tables of Satellite Imagery}

\subsection{\\Road Aggregation Schema}

\subsection{\\Input File Names According to SLEUTH Naming Convetion}

\subsection{\\Calibration Coefficients (OSM) of Coarse, Fine and Final Calibration}

\subsection{\\2030 Predictions}

enter image description here

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