2

I have this in my preamble:

%Number figures, eqns by chapter
\usepackage{chngcntr}
\counterwithin{figure}{chapter}
\counterwithin{equation}{chapter}

But all of my equations... even 3 or 4 chapters in, still have 0 as their primary number:

enter image description here

Any idea how I can fix this?

I am using Overleaf with a Tufte-style book template:

\documentclass{tufte-book}

\hypersetup{colorlinks}% uncomment this line if you prefer colored hyperlinks (e.g., for onscreen viewing)


%Number figures, eqns by chapter
\usepackage{chngcntr}
\counterwithin{figure}{chapter}
\counterwithin{equation}{chapter}

%%
% Book metadata
\title{A Tufte-Style Book\thanks{Thanks to Edward R.~Tufte for his inspiration.}}
\author[The Tufte-LaTeX Developers]{The Tufte-LaTeX\ Developers}
\publisher{Publisher of This Book}

%%
% If they're installed, use Bergamo and Chantilly from www.fontsite.com.
% They're clones of Bembo and Gill Sans, respectively.
%\IfFileExists{bergamo.sty}{\usepackage[osf]{bergamo}}{}% Bembo
%\IfFileExists{chantill.sty}{\usepackage{chantill}}{}% Gill Sans

%\usepackage{microtype}

%%
% Just some sample text
\usepackage{lipsum}

%%
% For nicely typeset tabular material
\usepackage{booktabs}

%%
% For graphics / images
\usepackage{graphicx}
\setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio}
\graphicspath{{graphics/}}

% The fancyvrb package lets us customize the formatting of verbatim
% environments.  We use a slightly smaller font.
\usepackage{fancyvrb}
\fvset{fontsize=\normalsize}

%%
% Prints argument within hanging parentheses (i.e., parentheses that take
% up no horizontal space).  Useful in tabular environments.
\newcommand{\hangp}[1]{\makebox[0pt][r]{(}#1\makebox[0pt][l]{)}}

%%
% Prints an asterisk that takes up no horizontal space.
% Useful in tabular environments.
\newcommand{\hangstar}{\makebox[0pt][l]{*}}

%%
% Prints a trailing space in a smart way.
\usepackage{xspace}

%%
% Some shortcuts for Tufte's book titles.  The lowercase commands will
% produce the initials of the book title in italics.  The all-caps commands
% will print out the full title of the book in italics.
\newcommand{\vdqi}{\textit{VDQI}\xspace}
\newcommand{\ei}{\textit{EI}\xspace}
\newcommand{\ve}{\textit{VE}\xspace}
\newcommand{\be}{\textit{BE}\xspace}
\newcommand{\VDQI}{\textit{The Visual Display of Quantitative Information}\xspace}
\newcommand{\EI}{\textit{Envisioning Information}\xspace}
\newcommand{\VE}{\textit{Visual Explanations}\xspace}
\newcommand{\BE}{\textit{Beautiful Evidence}\xspace}

\newcommand{\TL}{Tufte-\LaTeX\xspace}

% Prints the month name (e.g., January) and the year (e.g., 2008)
\newcommand{\monthyear}{%
  \ifcase\month\or January\or February\or March\or April\or May\or June\or
  July\or August\or September\or October\or November\or
  December\fi\space\number\year
}


% Prints an epigraph and speaker in sans serif, all-caps type.
\newcommand{\openepigraph}[2]{%
  %\sffamily\fontsize{14}{16}\selectfont
  \begin{fullwidth}
  \sffamily\large
  \begin{doublespace}
  \noindent\allcaps{#1}\\% epigraph
  \noindent\allcaps{#2}% author
  \end{doublespace}
  \end{fullwidth}
}

% Inserts a blank page
\newcommand{\blankpage}{\newpage\hbox{}\thispagestyle{empty}\newpage}

\usepackage{units}

% Typesets the font size, leading, and measure in the form of 10/12x26 pc.
\newcommand{\measure}[3]{#1/#2$\times$\unit[#3]{pc}}

% Macros for typesetting the documentation
\newcommand{\hlred}[1]{\textcolor{Maroon}{#1}}% prints in red
\newcommand{\hangleft}[1]{\makebox[0pt][r]{#1}}
\newcommand{\hairsp}{\hspace{1pt}}% hair space
\newcommand{\hquad}{\hskip0.5em\relax}% half quad space
\newcommand{\TODO}{\textcolor{red}{\bf TODO!}\xspace}
\newcommand{\ie}{\textit{i.\hairsp{}e.}\xspace}
\newcommand{\eg}{\textit{e.\hairsp{}g.}\xspace}
\newcommand{\na}{\quad--}% used in tables for N/A cells
\providecommand{\XeLaTeX}{X\lower.5ex\hbox{\kern-0.15em\reflectbox{E}}\kern-0.1em\LaTeX}
\newcommand{\tXeLaTeX}{\XeLaTeX\index{XeLaTeX@\protect\XeLaTeX}}
% \index{\texttt{\textbackslash xyz}@\hangleft{\texttt{\textbackslash}}\texttt{xyz}}
\newcommand{\tuftebs}{\symbol{'134}}% a backslash in tt type in OT1/T1
\newcommand{\doccmdnoindex}[2][]{\texttt{\tuftebs#2}}% command name -- adds backslash automatically (and doesn't add cmd to the index)
\newcommand{\doccmddef}[2][]{%
  \hlred{\texttt{\tuftebs#2}}\label{cmd:#2}%
  \ifthenelse{\isempty{#1}}%
    {% add the command to the index
      \index{#2 command@\protect\hangleft{\texttt{\tuftebs}}\texttt{#2}}% command name
    }%
    {% add the command and package to the index
      \index{#2 command@\protect\hangleft{\texttt{\tuftebs}}\texttt{#2} (\texttt{#1} package)}% command name
      \index{#1 package@\texttt{#1} package}\index{packages!#1@\texttt{#1}}% package name
    }%
}% command name -- adds backslash automatically
\newcommand{\doccmd}[2][]{%
  \texttt{\tuftebs#2}%
  \ifthenelse{\isempty{#1}}%
    {% add the command to the index
      \index{#2 command@\protect\hangleft{\texttt{\tuftebs}}\texttt{#2}}% command name
    }%
    {% add the command and package to the index
      \index{#2 command@\protect\hangleft{\texttt{\tuftebs}}\texttt{#2} (\texttt{#1} package)}% command name
      \index{#1 package@\texttt{#1} package}\index{packages!#1@\texttt{#1}}% package name
    }%
}% command name -- adds backslash automatically
\newcommand{\docopt}[1]{\ensuremath{\langle}\textrm{\textit{#1}}\ensuremath{\rangle}}% optional command argument
\newcommand{\docarg}[1]{\textrm{\textit{#1}}}% (required) command argument
\newenvironment{docspec}{\begin{quotation}\ttfamily\parskip0pt\parindent0pt\ignorespaces}{\end{quotation}}% command specification environment
\newcommand{\docenv}[1]{\texttt{#1}\index{#1 environment@\texttt{#1} environment}\index{environments!#1@\texttt{#1}}}% environment name
\newcommand{\docenvdef}[1]{\hlred{\texttt{#1}}\label{env:#1}\index{#1 environment@\texttt{#1} environment}\index{environments!#1@\texttt{#1}}}% environment name
\newcommand{\docpkg}[1]{\texttt{#1}\index{#1 package@\texttt{#1} package}\index{packages!#1@\texttt{#1}}}% package name
\newcommand{\doccls}[1]{\texttt{#1}}% document class name
\newcommand{\docclsopt}[1]{\texttt{#1}\index{#1 class option@\texttt{#1} class option}\index{class options!#1@\texttt{#1}}}% document class option name
\newcommand{\docclsoptdef}[1]{\hlred{\texttt{#1}}\label{clsopt:#1}\index{#1 class option@\texttt{#1} class option}\index{class options!#1@\texttt{#1}}}% document class option name defined
\newcommand{\docmsg}[2]{\bigskip\begin{fullwidth}\noindent\ttfamily#1\end{fullwidth}\medskip\par\noindent#2}
\newcommand{\docfilehook}[2]{\texttt{#1}\index{file hooks!#2}\index{#1@\texttt{#1}}}
\newcommand{\doccounter}[1]{\texttt{#1}\index{#1 counter@\texttt{#1} counter}}

% Generates the index
\usepackage{makeidx}
\makeindex

\begin{document}

% Front matter
\frontmatter

% r.1 blank page
\blankpage

% v.2 epigraphs
\newpage\thispagestyle{empty}
\openepigraph{%
The public is more familiar with bad design than good design.
It is, in effect, conditioned to prefer bad design, 
because that is what it lives with. 
The new becomes threatening, the old reassuring.
}{Paul Rand%, {\itshape Design, Form, and Chaos}
}
\vfill
\openepigraph{%
A designer knows that he has achieved perfection 
not when there is nothing left to add, 
but when there is nothing left to take away.
}{Antoine de Saint-Exup\'{e}ry}
\vfill
\openepigraph{%
\ldots the designer of a new system must not only be the implementor and the first 
large-scale user; the designer should also write the first user manual\ldots 
If I had not participated fully in all these activities, 
literally hundreds of improvements would never have been made, 
because I would never have thought of them or perceived 
why they were important.
}{Donald E. Knuth}


% r.3 full title page
\maketitle


% v.4 copyright page
\newpage
\begin{fullwidth}
~\vfill
\thispagestyle{empty}
\setlength{\parindent}{0pt}
\setlength{\parskip}{\baselineskip}
Copyright \copyright\ \the\year\ \thanklessauthor

\par\smallcaps{Published by \thanklesspublisher}

\par\smallcaps{tufte-latex.googlecode.com}

\par Licensed under the Apache License, Version 2.0 (the ``License''); you may not
use this file except in compliance with the License. You may obtain a copy
of the License at \url{http://www.apache.org/licenses/LICENSE-2.0}. Unless
required by applicable law or agreed to in writing, software distributed
under the License is distributed on an \smallcaps{``AS IS'' BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF ANY KIND}, either express or implied. See the
License for the specific language governing permissions and limitations
under the License.\index{license}

\par\textit{First printing, \monthyear}
\end{fullwidth}

% r.5 contents
\tableofcontents

\listoffigures

\listoftables

% r.7 dedication
\cleardoublepage
~\vfill
\begin{doublespace}
\noindent\fontsize{18}{22}\selectfont\itshape
\nohyphenation
Dedicated to those who appreciate \LaTeX{} 
and the work of \mbox{Edward R.~Tufte} 
and \mbox{Donald E.~Knuth}.
\end{doublespace}
\vfill
\vfill


% r.9 introduction
\cleardoublepage
\chapter*{Introduction}

This sample book discusses the design of Edward Tufte's
books\cite{Tufte2001,Tufte1990,Tufte1997,Tufte2006}
and the use of the \doccls{tufte-book} and \doccls{tufte-handout} document classes.


%%
% Start the main matter (normal chapters)
\mainmatter


\chapter{The Design of Tufte's Books}
\label{ch:tufte-design}

\chapter{Two}

\chapter{Three}

\begin{equation}
    y=mx+b
\end{equation}





\backmatter

\bibliography{sample-handout}
\bibliographystyle{plainnat}


\printindex

\end{document}
1

tufte-book's \chapters aren't numbered by default. The reason for this is because the document class sets the counter secnumdepth to -1 (in line 495 of \input{tufte-common.def}). Why is this important? Chapters are defined at sectional level 0, and with a secnumdepth set to -1, chapters are numbered. Moreover, chapter counters aren't incremented. That's why your chapter reference remains at 0.

To overcome this, you can manually increment the chapter counter (using \refstepcounter{chapter} after \chapters, not a \chapter*) or automatically via the following patch:

\usepackage{etoolbox}
\makeatletter
\patchcmd{\Hy@org@chapter}% <cmd>
  {\ifnum}% <search>
  {\refstepcounter{chapter}\ifnum}% <replace>
  {}{}% <success><failure>
\makeatother

enter image description here

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