notes-epland.tex

%-----------------------------------------------------------------------------%
% Set metadata for use with pdfx
%\begingroup\newif\ifmy
%\IfFileExists{\jobname.xmpdata}{}{\mytrue}
%\ifmy
%\begin{filecontents*}{\jobname.xmpdata}
%\Title{Data Science Notes}
%\Author{Matthew Epland, Ph.D.}
%\Keywords{Data Science\sep Machine Learning\sep Statistics}
%\Copyright{CC-BY-4.0}
%\end{filecontents*}
%\fi\endgroup

% https://tex.stackexchange.com/questions/52317/pdftex-warning-version-allowed
% https://tex.stackexchange.com/questions/301386/why-is-1-5-the-default-pdf-version
% https://tex.stackexchange.com/a/375018
\directlua{pdf.setminorversion(6)}

% \Subject{TODO}

% https://tex.stackexchange.com/a/572817
\RequirePackage{silence}
\WarningFilter{latexfont}{Font shape}
\WarningFilter{latexfont}{Some font shapes were}

%-----------------------------------------------------------------------------%
% Set documentclass
\documentclass[nogradschool,singlespace,nobind]{dukedissertation_modified}

%-----------------------------------------------------------------------------%
% usepackages
\usepackage{amsmath,amssymb,bbm,bm} % https://ctan.org/pkg/bm
\usepackage{mathtools}
\usepackage{cancel}
\usepackage{graphicx}
\usepackage{xcolor}
\usepackage[TU,T1]{fontenc}
\usepackage{indentfirst}
\usepackage{textcomp} % needed to fix \mico \textmu from siunitx to work with microtype: https://tex.stackexchange.com/questions/74670/microtype-siunitx-and-micro-mysterious-warnings
\usepackage[protrusion=true,expansion=true]{microtype} % make text flow nicely... might screw up duke dissertation template
\usepackage{verbatim} % verbatim text and comment environment
\usepackage{lmodern} % allowing font sizes at arbitrary sizes
\DeclareFontShape{TU}{lmr}{bx}{sc} { <-> ssub * lmr/bx/n }{} % https://tex.stackexchange.com/questions/22240/choosing-font-for-bold-small-caps-or-any-other-particular-familyseriesshape-c]
\usepackage{notoccite} % fixes citation numbering in captions with respect to lof & lot, see https://ctan.org/pkg/notoccite
\usepackage[nocompress]{cite} % orders references numerically within one \cite{}, see https://tex.stackexchange.com/questions/69230/numbered-ordering-of-multiple-citations Also changes spacing after comma
\usepackage{fnpct} % make multiple footnotes at one point look nice, https://tex.stackexchange.com/questions/28465/multiple-footnotes-at-one-point
\usepackage[separate-uncertainty,multi-part-units=single,free-standing-units,product-units=repeat,use-xspace]{siunitx} % units package, see https://www.ctan.org/pkg/siunitx
\sisetup{range-phrase={\text{--}},range-units=single}
\usepackage{physics}
% silence warning about qty conflict
% https://tex.stackexchange.com/a/681701
\ExplSyntaxOn
\msg_redirect_name:nnn { siunitx } { physics-pkg } { none }
\ExplSyntaxOff
\usepackage{booktabs,array,multirow,diagbox}
\renewcommand{\arraystretch}{1.5} % gives extra height to tabular rows for super/subscripts
%\usepackage{longtable}
\usepackage{enumitem}
\usepackage{lscape} % landscape https://ctan.org/pkg/lscape
\usepackage{moresize}
\usepackage{fontawesome}
\usepackage{listings}
% https://tex.stackexchange.com/a/224098
\lstdefinelanguage{SQL_extended}{language=SQL,
morekeywords={
ARRAY_CONSTRUCT,
ARRAY_CONSTRUCT_COMPACT,
ARRAYS_OVERLAP,
CONCAT,
DATEDIFF,
FLATTEN,
FOR,
GENERATE_ARRAY,
IFF,
IS,
LAG,
LATERAL,
LEAD,
OVER,
PARTITION,
PIVOT,
QUALIFY,
REPLACE,
ROW_NUMBER,
STRING,
UNNEST,
WINDOW,
WITH
}}
\lstnewenvironment{SQLcode}{\lstset{language=SQL_extended}}{}

% for algorithms
\usepackage{algorithm}
\usepackage{algorithmicx}
\usepackage[noend]{algpseudocode}
\algdef{SE}[DOWHILE]{Do}{doWhile}{\algorithmicdo}[1]{\algorithmicwhile\ #1}%
\renewcommand\algorithmicdo{}
\newcommand{\CommentInline}[1]{\STATE \textcolor{gray}{\# #1}}

\usepackage[top=1in, bottom=1.25in, left=1.25in, right=1.25in]{geometry}
\usepackage{fancyhdr}
\pagestyle{plain}

% use subcaption to get split figures, but the caption dependency doesn't know about the dukedissertation document class - turn off the warning with silence
% load caption explicitly first to set it's options, subcaption says it passes them through but it doesn't seem to work
% https://tex.stackexchange.com/questions/34579/is-there-really-something-wrong-with-using-the-caption-package-for-continuedflo
% https://en.wikibooks.org/wiki/LaTeX/Floats,_Figures_and_Captions#Subfloats
% https://ctan.org/pkg/caption
% https://ctan.org/pkg/subcaption
\usepackage{silence}
\WarningFilter{caption}{Unknown document class}
\WarningFilter{caption}{Unsupported document class}
\WarningFilter{hyperref}{The PDF version number could not be set}
\usepackage{setspace} % needed to specify, https://ctan.org/pkg/setspace
\usepackage[style=base,skip=2pt,width=\textwidth]{caption} % ,font={stretch=1.3}
\usepackage[skip=1pt]{subcaption}
\newcommand\mysubref[1]{(\subref{#1})} % create mysubfigure command to reference subfigures from within the main caption, without messing with the normal \cref formatting. Adapted from https://tex.stackexchange.com/a/131366
\newsavebox{\largestimage} % see https://tex.stackexchange.com/questions/239128/subcaption-vertical-alignment-of-two-images-of-different-vertical-size

%\renewcommand{\GenericWarning}[2]{\GenericError{#1}{#2}{}{This warning has been turned into a fatal error.}} % crash on warnings for debugging https://stackoverflow.com/a/3277465

% Don't let floats get before the subsection where they're included
% https://tex.stackexchange.com/questions/32598/force-latex-image-to-appear-in-the-section-in-which-its-declared
% https://tex.stackexchange.com/questions/279/how-do-i-ensure-that-figures-appear-in-the-section-theyre-associated-with/235312#235312
% Also doesn't let a float go into a following subsection, results in a ton of blank space - probably better left off
% \usepackage{placeins}
%\let\Oldsubsection\subsection
%\renewcommand{\subsection}{\FloatBarrier\Oldsubsection}

\usepackage{float} % to allow for H option. Works better than \FloatBarrier from placeins, though it is more manual
\floatstyle{plaintop}
\restylefloat{table}

% keep footnotes from splitting, can still happen sometimes (10000 forces)
% https://tex.stackexchange.com/questions/32208/footnote-runs-onto-second-page
\interfootnotelinepenalty=9999

% keep inline equations from splitting, can still happen sometimes (10000 forces)
% https://tex.stackexchange.com/a/14243
\relpenalty=9999
\binoppenalty=9999

% center subfigure captions with multiple lines
\captionsetup[subfigure]{justification=centering}

%-----------------------------------------------------------------------------%
% Other possibly useful packages
% \usepackage{fancyvrb}
% \usepackage{ulem}
% \usepackage{overpic}
% \usepackage{amsfonts, amsthm}
% \usepackage{mathabx}

%-----------------------------------------------------------------------------%
% tweak listings
\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codemauve}{rgb}{0.58,0,0.82}

\lstset{
  backgroundcolor=\color{white},     % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}; should come as last argument
  % basicstyle=\ssmall,              % the size of the fonts that are used for the code
  basicstyle=\ttfamily,              % make font tt
  upquote=true,                      % make all single quotes straight up and down
  breakatwhitespace=false,           % sets if automatic breaks should only happen at whitespace
  breaklines=true,                   % sets automatic line breaking
  captionpos=b,                      % sets the caption-position to bottom
  commentstyle=\color{codegreen},    % comment style
  % deletekeywords={...},            % if you want to delete keywords from the given language
  % escapeinside={\%*}{*)},          % if you want to add LaTeX within your code
  extendedchars=true,                % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
  firstnumber=1,                     % start line enumeration with line 1
  frame=none,                        % adds a frame around the code
  keepspaces=true,                   % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
  keywordstyle=\color{blue},         % keyword style
  % language=Octave,                 % the language of the code
  % morekeywords={*,...},            % if you want to add more keywords to the set
  numbers=left,                      % where to put the line-numbers; possible values are (none, left, right)
  numbersep=5pt,                     % how far the line-numbers are from the code
  numberstyle=\ttfamily\tiny\color{codegray}, % the style that is used for the line-numbers
  rulecolor=\color{black},           % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
  showspaces=false,                  % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
  showstringspaces=false,            % underline spaces within strings only
  showtabs=false,                    % show tabs within strings adding particular underscores
  stepnumber=1,                      % the step between two line-numbers. If it's 1, each line will be numbered
  stringstyle=\color{codemauve},     % string literal style
  tabsize=2,                         % sets default tabsize to 2 spaces
}

%-----------------------------------------------------------------------------%
% Include abbreviations
\input{abbreviations.tex}

%-----------------------------------------------------------------------------%
% Include tikz figures which can not be made standalone, only if they have internal references / citations. Also must be manually added to Makefile if they use feynmp
\usepackage{tikz}

%-----------------------------------------------------------------------------%
% Theorem, Lemma, etc. environments
%\newtheorem{theorem}{Theorem}%[section]
%\newtheorem{lemma}[theorem]{Lemma}
%\newtheorem{proposition}[theorem]{Proposition}
%\newtheorem{corollary}[theorem]{Corollary}
%\newtheorem{result}[theorem]{Result}

%-----------------------------------------------------------------------------%
% PREAMBLE
%-----------------------------------------------------------------------------%
\author{Matthew Epland, Ph.D.}
\title{Data Science Notes}
\date{\today}
%-----------------------------------------------------------------------------%

%-----------------------------------------------------------------------------%
% HYPERREF
%-----------------------------------------------------------------------------%
\usepackage[hyperpageref]{backref} % pages

% need to load in this order to get proper pdfx a-2b format!!!
\PassOptionsToPackage{hyperfootnotes,pagebackref}{hyperref}

% comment out \usepackage{hyperref} and \hypersetup if using pdfx
\usepackage{hyperref}
\makeatletter\hypersetup{
    breaklinks, baseurl=http://, pdfborder=0 0 0, pdfpagemode=UseNone, pdfstartpage=1, bookmarksopen=false, bookmarksdepth=2, % to show sections and subsections
    pdfauthor      = {Matthew Epland, Ph.D.}, %
    pdftitle       = {Data Science Notes}, %
    pdfsubject     = {Data Science, Machine Learning, Statistics}, %
    pdfkeywords    = {Data Science, Machine Learning, Statistics}
}\makeatother

% \usepackage[a-2b]{pdfx} % Note pdfx does not work with travis CI due to latest ubuntu image being from 2016, thus containing this bug https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=877167 fixed in oct 2017. Can use locally if desired

\hypersetup{plainpages=false, bookmarksnumbered,
            % draft, % for printing
            colorlinks, linkcolor=blue, citecolor=blue, urlcolor=blue, % for web
            % breaklinks=true,
           }

% adapted from https://tex.stackexchange.com/questions/183702/formatting-back-references-in-bibliography-bibtex
\renewcommand*{\backrefalt}[4]{%
%    \ifcase #1 Not cited.%
    \ifcase #1% Not cited.%
          \or Cited on page~#2.%
          \else Cited on pages #2.%
    \fi%
    }

%-----------------------------------------------------------------------------%
% use cref and not ref, have to load last
\usepackage[capitalise]{cleveref} % https://ctan.org/pkg/cleveref see section 7.1, if redefining need to make them caps
\crefname{figure}{Figure}{Figures}
\Crefname{figure}{Figure}{Figures}
\crefname{tabular}{Table}{Tables}
\Crefname{tabular}{Table}{Tables}
\crefname{section}{Section}{Sections}
\Crefname{section}{Section}{Sections}
\crefname{chapter}{Chapter}{Chapters}
\Crefname{chapter}{Chapter}{Chapters}
\crefname{appchap}{Appendix}{Appendices}
\Crefname{appchap}{Appendix}{Appendices}
\crefformat{equation}{(#2#1#3)}

\newcommand\preface{%
   \nmchapter{Preface}
}

\begin{document}

%-----------------------------------------------------------------------------%
% TITLE PAGE
%-----------------------------------------------------------------------------%
\maketitle

%-----------------------------------------------------------------------------%
% ABSTRACT -- included file should start with '\abstract'.
%-----------------------------------------------------------------------------%
% \include{{sections/abstract}}

%-----------------------------------------------------------------------------%
% FRONTMATTER
%-----------------------------------------------------------------------------%
\tableofcontents % Automatically generated
\backrefsetup{disable}
\include{{sections/listofabbr}} % List of Abbreviations. Start file with '\abbreviations'
\backrefsetup{enable}

%-----------------------------------------------------------------------------%
% PREFACE
%-----------------------------------------------------------------------------%
\include{{sections/preface}}

%==============================================================================
%-----------------------------------------------------------------------------%
%
% MAIN BODY
%
%
%-----------------------------------------------------------------------------%
\include{{sections/stats}}
\include{{sections/hypo}}
\include{{sections/regression}}
\include{{sections/ml_general}}
\include{{sections/dim_reduct}}
\include{{sections/opt}}
\include{{sections/class}}
\include{{sections/cluster}}
\include{{sections/time_series}}
\include{{sections/survival}}
\include{{sections/causality}}
\include{{sections/misc}}

%==============================================================================

%-----------------------------------------------------------------------------%
% APPENDICES -- OPTIONAL. These are just chapters enumerated by Appendix A, Appendix B, Appendix C...
%-----------------------------------------------------------------------------%
% Start each appendix tex file with '\chapter{Title}'
\appendix
\include{{sections/appendixes/pandas}}
\include{{sections/appendixes/sql}}
\include{{sections/appendixes/pyspark}}
\include{{sections/appendixes/coding}}
\include{{sections/appendixes/distributions}}
%\include{{sections/appendixes/finance}}

%-----------------------------------------------------------------------------%
% BIBLIOGRAPHY -- Change the style to match your discipline's standards.
%-----------------------------------------------------------------------------%
\bibliographystyle{./bib/atlasBibStyleWithTitle}
\cleardoublepage
\normalbaselines %Fixes spacing of bibliography
% \addcontentsline{toc}{chapter}{Bibliography} % not needed on my system
\bibliography{./bib/bib}
%-----------------------------------------------------------------------------%

%-----------------------------------------------------------------------------
\end{document}