% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
]{article}
\title{Test}
\author{Tim Bergsma}
\date{2022-04-18}

\usepackage{amsmath,amssymb}
\usepackage{lmodern}
\usepackage{iftex}
\ifPDFTeX
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
  \usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
  \usepackage{unicode-math}
  \defaultfontfeatures{Scale=MatchLowercase}
  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
  \usepackage[]{microtype}
  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
  \IfFileExists{parskip.sty}{%
    \usepackage{parskip}
  }{% else
    \setlength{\parindent}{0pt}
    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
  \KOMAoptions{parskip=half}}
\makeatother
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\hypersetup{
  pdftitle={Test},
  pdfauthor={Tim Bergsma},
  hidelinks,
  pdfcreator={LaTeX via pandoc}}
\urlstyle{same} % disable monospaced font for URLs
\usepackage[margin=1in]{geometry}
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
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\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
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\usepackage{graphicx}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
% Set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{array}
\usepackage{multirow}
\usepackage{wrapfig}
\usepackage{float}
\usepackage{colortbl}
\usepackage{pdflscape}
\usepackage{tabu}
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage[normalem]{ulem}
\usepackage{makecell}
\usepackage{xcolor}
\ifLuaTeX
  \usepackage{selnolig}  % disable illegal ligatures
\fi

\begin{document}
\maketitle

{
\setcounter{tocdepth}{2}
\tableofcontents
}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(tablet)}
\FunctionTok{library}\NormalTok{(haven)}
\FunctionTok{library}\NormalTok{(yamlet)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Attaching package: 'yamlet'
\end{verbatim}

\begin{verbatim}
## The following object is masked from 'package:stats':
## 
##     filter
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(magrittr)}
\FunctionTok{library}\NormalTok{(dplyr)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Attaching package: 'dplyr'
\end{verbatim}

\begin{verbatim}
## The following objects are masked from 'package:stats':
## 
##     filter, lag
\end{verbatim}

\begin{verbatim}
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(kableExtra)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Attaching package: 'kableExtra'
\end{verbatim}

\begin{verbatim}
## The following object is masked from 'package:dplyr':
## 
##     group_rows
\end{verbatim}

\begin{verbatim}
## The following object is masked from 'package:yamlet':
## 
##     footnote
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(knitr)}

\CommentTok{\# make adsl with imputed bmi, imputed race, and two{-}row footnote}
\NormalTok{x }\OtherTok{\textless{}{-}} \FunctionTok{read\_sas}\NormalTok{(}\StringTok{\textquotesingle{}adsl.sas7bdat\textquotesingle{}}\NormalTok{)}
\NormalTok{m }\OtherTok{\textless{}{-}} \FunctionTok{read\_yamlet}\NormalTok{(}\StringTok{\textquotesingle{}adsl.yaml\textquotesingle{}}\NormalTok{)}

\CommentTok{\# https://github.com/haozhu233/kableExtra/issues/703}
\FunctionTok{names}\NormalTok{(m}\SpecialCharTok{$}\NormalTok{race}\SpecialCharTok{$}\NormalTok{guide)[[}\DecValTok{3}\NormalTok{]] }\OtherTok{\textless{}{-}} \StringTok{\textquotesingle{}Oriental\textquotesingle{}}

\CommentTok{\# fortify to mimic app.R}
\NormalTok{have }\OtherTok{\textless{}{-}} \FunctionTok{names}\NormalTok{(x)}
\NormalTok{need }\OtherTok{\textless{}{-}} \FunctionTok{names}\NormalTok{(m)}
\NormalTok{make }\OtherTok{\textless{}{-}} \FunctionTok{setdiff}\NormalTok{(need, have)}
\ControlFlowTok{for}\NormalTok{(col }\ControlFlowTok{in}\NormalTok{ make) x[[col]] }\OtherTok{\textless{}{-}} \FunctionTok{rep}\NormalTok{(}\ConstantTok{NA\_integer\_}\NormalTok{, }\FunctionTok{nrow}\NormalTok{(x))}

\CommentTok{\# ensure positive nrow}
\ControlFlowTok{if}\NormalTok{(}\FunctionTok{nrow}\NormalTok{(x) }\SpecialCharTok{==} \DecValTok{0}\NormalTok{) x }\OtherTok{\textless{}{-}}\NormalTok{ x[}\StringTok{\textquotesingle{}\textquotesingle{}}\NormalTok{,,drop }\OtherTok{=} \ConstantTok{FALSE}\NormalTok{]}

\CommentTok{\# drop unspecified}
\NormalTok{x }\SpecialCharTok{\%\textless{}\textgreater{}\%} \FunctionTok{select}\NormalTok{(}\SpecialCharTok{!!!}\FunctionTok{names}\NormalTok{(m))}

\CommentTok{\# apply meta}
\NormalTok{x }\OtherTok{\textless{}{-}} \FunctionTok{redecorate}\NormalTok{(x, m)}

\CommentTok{\# \# Promote NA to a level of the factor}
\CommentTok{\# x \%\textless{}\textgreater{}\% resolve(exclude = NULL)}
\NormalTok{x }\SpecialCharTok{\%\textless{}\textgreater{}\%} \FunctionTok{resolve}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## Warning in match.fun(test)(val, data = data[[i]], ...): data has values not in
## Placebo, TRT 10 mg, TRT 20 mg: e.g.
\end{verbatim}

\begin{verbatim}
## Warning in match.fun(test)(val, data = data[[i]], ...): data has values not in
## Placebo, TRT 10 mg, TRT 20 mg, TRT Total: e.g.
\end{verbatim}

\begin{verbatim}
## Warning in match.fun(test)(val, data = data[[i]], ...): data has values not in
## White, Black, Asian, Other, : e.g. NA
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{foot }\OtherTok{\textless{}{-}}
\StringTok{\textquotesingle{}a clinicaltrial.gov}
\StringTok{b some other comment\textquotesingle{}}
\FunctionTok{options}\NormalTok{(}\AttributeTok{knitr.kable.NA =} \DecValTok{0}\NormalTok{)}
\CommentTok{\#opts\_knit$set(out.format = \textquotesingle{}latex\textquotesingle{})}
\CommentTok{\# debug(tablet:::widgets.devalued)}
\CommentTok{\#x \%\textgreater{}\% group\_by(trt01a, trt01aa) \%\textgreater{}\% select(race) \%\textgreater{}\% tablet}
\NormalTok{x}\SpecialCharTok{$}\NormalTok{trt01a[] }\OtherTok{\textless{}{-}} \ConstantTok{NA}
\NormalTok{x}\SpecialCharTok{$}\NormalTok{trt01aa[] }\OtherTok{\textless{}{-}} \ConstantTok{NA}
\CommentTok{\#debug(categoricals)}
\CommentTok{\#debug(numerics)}
\CommentTok{\#debug(groupfull)}
\NormalTok{x }\OtherTok{\textless{}{-}}\NormalTok{ x }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{filter}\NormalTok{(saffl }\SpecialCharTok{==} \StringTok{\textquotesingle{}Y\textquotesingle{}}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{group\_by}\NormalTok{(trt01a, trt01aa) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{select}\NormalTok{(}
  \CommentTok{\#  age, agegr, sex, weight, bmi,}
\NormalTok{    race, bmi}
\NormalTok{  ) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{splice}\NormalTok{(}
    \AttributeTok{all\_levels =} \ConstantTok{TRUE}\NormalTok{,}
    \AttributeTok{fun =} \FunctionTok{list}\NormalTok{(}
\NormalTok{      sum }\SpecialCharTok{\textasciitilde{}}  \FunctionTok{sum}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{),}
\NormalTok{      pct }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,     sum }\SpecialCharTok{/}\NormalTok{ n }\SpecialCharTok{*} \DecValTok{100}\NormalTok{        ),}
\NormalTok{      ave }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,    }\FunctionTok{mean}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{)),}
\NormalTok{      std }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,      }\FunctionTok{sd}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{)),}
\NormalTok{      med }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,  }\FunctionTok{median}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{)),}
\NormalTok{      min }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,     }\FunctionTok{min}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{)),}
\NormalTok{      max }\SpecialCharTok{\textasciitilde{}} \FunctionTok{signif}\NormalTok{(}\AttributeTok{digits =} \DecValTok{3}\NormalTok{,     }\FunctionTok{max}\NormalTok{(x,  }\AttributeTok{na.rm =} \ConstantTok{TRUE}\NormalTok{)),}
\NormalTok{      smn }\SpecialCharTok{\textasciitilde{}} \FunctionTok{sum}\NormalTok{(}\SpecialCharTok{!}\FunctionTok{is.na}\NormalTok{(x))}
\NormalTok{    ),}
    \AttributeTok{num =} \FunctionTok{list}\NormalTok{(}
\NormalTok{      n }\SpecialCharTok{\textasciitilde{}}\NormalTok{ smn,}
      \StringTok{\textasciigrave{}}\AttributeTok{Mean (SD)}\StringTok{\textasciigrave{}} \SpecialCharTok{\textasciitilde{}}\NormalTok{  ave }\SpecialCharTok{+} \StringTok{\textquotesingle{} (\textquotesingle{}} \SpecialCharTok{+}\NormalTok{ std }\SpecialCharTok{+} \StringTok{\textquotesingle{})\textquotesingle{}}\NormalTok{,}
\NormalTok{      Median }\SpecialCharTok{\textasciitilde{}}  \FunctionTok{paste}\NormalTok{(med),}
      \StringTok{\textasciigrave{}}\AttributeTok{Min, Max}\StringTok{\textasciigrave{}} \SpecialCharTok{\textasciitilde{}}\NormalTok{  min }\SpecialCharTok{+} \StringTok{\textquotesingle{}, \textquotesingle{}} \SpecialCharTok{+}\NormalTok{ max}
\NormalTok{    ),}
    \AttributeTok{fac =} \FunctionTok{list}\NormalTok{(}
      \StringTok{\textasciigrave{}}\AttributeTok{ }\StringTok{\textasciigrave{}} \SpecialCharTok{\textasciitilde{}} \FunctionTok{ifelse}\NormalTok{(sum }\SpecialCharTok{==} \DecValTok{0}\NormalTok{, }\StringTok{\textquotesingle{}0\textquotesingle{}}\NormalTok{, sum }\SpecialCharTok{+} \StringTok{\textquotesingle{} (\textquotesingle{}} \SpecialCharTok{+}\NormalTok{ pct }\SpecialCharTok{+} \StringTok{\textquotesingle{}\%\textquotesingle{}} \SpecialCharTok{+} \StringTok{\textquotesingle{})\textquotesingle{}}\NormalTok{)}
\NormalTok{    )}
\NormalTok{  )}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## Adding missing grouping variables: `trt01a`, `trt01aa`
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\# remove NA groups}
\NormalTok{na }\OtherTok{\textless{}{-}} \FunctionTok{which}\NormalTok{(}\FunctionTok{names}\NormalTok{(x) }\SpecialCharTok{==} \StringTok{\textquotesingle{}NA\textquotesingle{}}\NormalTok{)}
\ControlFlowTok{for}\NormalTok{(i }\ControlFlowTok{in} \FunctionTok{rev}\NormalTok{(na))x[[na]] }\OtherTok{\textless{}{-}} \ConstantTok{NULL}

\CommentTok{\# reverse lookup on make}
\NormalTok{codelist }\OtherTok{\textless{}{-}} \FunctionTok{attr}\NormalTok{(x}\SpecialCharTok{$}\StringTok{\textasciigrave{}}\AttributeTok{\_tablet\_name}\StringTok{\textasciigrave{}}\NormalTok{, }\StringTok{\textquotesingle{}codelist\textquotesingle{}}\NormalTok{)}
\NormalTok{x}\SpecialCharTok{$}\StringTok{\textasciigrave{}}\AttributeTok{\_tablet\_original}\StringTok{\textasciigrave{}} \OtherTok{\textless{}{-}} \FunctionTok{unlist}\NormalTok{(codelist[x}\SpecialCharTok{$}\StringTok{\textasciigrave{}}\AttributeTok{\_tablet\_name}\StringTok{\textasciigrave{}}\NormalTok{])}
\CommentTok{\# very elegant, but blows away attributes}
\CommentTok{\# x \%\textless{}\textgreater{}\% mutate(}
\CommentTok{\#   across(}
\CommentTok{\#     .cols = {-}starts\_with(\textquotesingle{}\_tablet\_\textquotesingle{}),}
\CommentTok{\#     .fns = \textasciitilde{} ifelse(\textasciigrave{}\_tablet\_original\textasciigrave{} \%in\% names(conf$imputed), \textquotesingle{}{-}\textquotesingle{}, .x)}
\CommentTok{\#   )}
\CommentTok{\# )}
\NormalTok{targets }\OtherTok{\textless{}{-}} \FunctionTok{seq\_along}\NormalTok{(x)[}\SpecialCharTok{!}\NormalTok{(}\FunctionTok{grepl}\NormalTok{(}\StringTok{\textquotesingle{}\_tablet\_\textquotesingle{}}\NormalTok{, }\FunctionTok{names}\NormalTok{(x)))]}
\NormalTok{imputed }\OtherTok{\textless{}{-}}\NormalTok{ x}\SpecialCharTok{$}\StringTok{\textasciigrave{}}\AttributeTok{\_tablet\_original}\StringTok{\textasciigrave{}} \SpecialCharTok{\%in\%}\NormalTok{ make}
\ControlFlowTok{if}\NormalTok{(}\FunctionTok{length}\NormalTok{(imputed) }\SpecialCharTok{\&} \FunctionTok{length}\NormalTok{(targets)) x[imputed, targets] }\OtherTok{\textless{}{-}} \StringTok{\textquotesingle{}{-}\textquotesingle{}}
\NormalTok{x}\SpecialCharTok{$}\StringTok{\textasciigrave{}}\AttributeTok{\_tablet\_original}\StringTok{\textasciigrave{}} \OtherTok{\textless{}{-}} \ConstantTok{NULL}

\NormalTok{x }\SpecialCharTok{\%\textgreater{}\%}
\NormalTok{  as\_kable }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{footnote}\NormalTok{(}
    \AttributeTok{general =} \CommentTok{\# escape\_latex(}
      \FunctionTok{c}\NormalTok{(}\StringTok{\textquotesingle{}a something\textquotesingle{}}\NormalTok{,}\StringTok{\textquotesingle{}b something\textquotesingle{}}\NormalTok{)}
      \CommentTok{\# )}
\NormalTok{    ,}
    \AttributeTok{fixed\_small\_size =} \ConstantTok{TRUE}\NormalTok{,}
    \AttributeTok{general\_title =} \StringTok{" "}\NormalTok{,}
    \AttributeTok{threeparttable =} \ConstantTok{TRUE}
\NormalTok{  ) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{kable\_styling}\NormalTok{(}\AttributeTok{latex\_options =} \StringTok{\textquotesingle{}scale\_down\textquotesingle{}}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{table}
\centering
\begin{threeparttable}
\resizebox{\linewidth}{!}{
\begin{tabular}[t]{llllll}
\toprule
  & \makecell[c]{Placebo\\(N = 0)} & \makecell[c]{TRT 10 mg\\(N = 0)} & \makecell[c]{TRT 20 mg\\(N = 0)} & \makecell[c]{TRT Total\\(N = 0)} & \makecell[c]{All\\(N = 12)}\\
\midrule
\addlinespace[0.3em]
\multicolumn{6}{l}{\textbf{Race}}\\
\hspace{1em}White & - & - & - & - & -\\
\hspace{1em}Black & - & - & - & - & -\\
\hspace{1em}Oriental & - & - & - & - & -\\
\hspace{1em}Other & - & - & - & - & -\\
\hspace{1em}Missing & - & - & - & - & -\\
\addlinespace[0.3em]
\multicolumn{6}{l}{\textbf{Body Mass Index}}\\
\hspace{1em}n & - & - & - & - & -\\
\hspace{1em}Mean (SD) & - & - & - & - & -\\
\hspace{1em}Median & - & - & - & - & -\\
\hspace{1em}Min, Max & - & - & - & - & -\\
\bottomrule
\end{tabular}}
\begin{tablenotes}
\small
\item \textit{ } 
\item a something
\item b something
\end{tablenotes}
\end{threeparttable}
\end{table}

\end{document}
