[Tex/LaTex] Table spacing issue converting to PDF via LaTeX with pandoc

knitrpandocrtables

In the application of Rmarkdown I often found my answers concerning “LaTeX” and “pandoc” here at TeX Stackexchange. For that reason I want to repeat here my question I asked at stackoverflow hoping to find a solution to following issue while converting to PDF via LaTeX with pandoc:

I'm facing the issue that in R texreg() doesn't seem to break the lines in the notes below the table. Also the margins between the models are not extended equally like it's happening with htmlreg() which gives a clean result. Manual breaks like \n or HTML tags are not working with 'texreg'. There's a partly workaround from MichaelChirico, but one has to change the texreg() function but it seems the method doesn't respect the case when we're dealing with more than one model side by side.

Here is the code I'm using:

---
title: "Untitled"
author: "jaySf"
date: "13 Juni 2017"
output:
  pdf_document: default
  html_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r results="asis"}
library(car)
lm1 <- lm(prestige ~ income, data=Duncan)
lm2 <- lm(prestige ~ education, data=Duncan)
lm3 <- lm(prestige ~ income + education, data=Duncan)

library(texreg)
texreg(list(lm1, lm2, lm3), custom.note = "Lorem ipsum dolor sit amet, <br>consetetur sadipscing 
       elitr, sed diam. %stars.") # for pdf output

htmlreg(list(lm1, lm2, lm3), custom.note = "Lorem ipsum dolor sit amet, <br>consetetur sadipscing 
       elitr, sed diam. %stars.") # for html output
```

And this is the output:

Does anybody have a clue? Any help is appreciated.

And here the LaTeX code which is produced:

\documentclass[]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\usepackage[margin=1in]{geometry}
\usepackage{hyperref}
\hypersetup{unicode=true,
            pdftitle={Untitled},
            pdfauthor={jaySf},
            pdfborder={0 0 0},
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
\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{\KeywordTok}[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{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\ImportTok}[1]{{#1}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{{#1}}}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{{#1}}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{{#1}}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{{#1}}}}
\newcommand{\BuiltInTok}[1]{{#1}}
\newcommand{\ExtensionTok}[1]{{#1}}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{{#1}}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{{#1}}}
\newcommand{\RegionMarkerTok}[1]{{#1}}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{{#1}}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\NormalTok}[1]{{#1}}
\usepackage{graphicx,grffile}
\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}
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi

%%% Use protect on footnotes to avoid problems with footnotes in titles
\let\rmarkdownfootnote\footnote%
\def\footnote{\protect\rmarkdownfootnote}

%%% Change title format to be more compact
\usepackage{titling}

% Create subtitle command for use in maketitle
\newcommand{\subtitle}[1]{
  \posttitle{
    \begin{center}\large#1\end{center}
    }
}

\setlength{\droptitle}{-2em}
  \title{Untitled}
  \pretitle{\vspace{\droptitle}\centering\huge}
  \posttitle{\par}
  \author{jaySf}
  \preauthor{\centering\large\emph}
  \postauthor{\par}
  \predate{\centering\large\emph}
  \postdate{\par}
  \date{13 Juni 2017}


\begin{document}
\maketitle

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(car)}
\NormalTok{lm1 <-}\StringTok{ }\KeywordTok{lm}\NormalTok{(prestige ~}\StringTok{ }\NormalTok{income, }\DataTypeTok{data=}\NormalTok{Duncan)}
\NormalTok{lm2 <-}\StringTok{ }\KeywordTok{lm}\NormalTok{(prestige ~}\StringTok{ }\NormalTok{education, }\DataTypeTok{data=}\NormalTok{Duncan)}
\NormalTok{lm3 <-}\StringTok{ }\KeywordTok{lm}\NormalTok{(prestige ~}\StringTok{ }\NormalTok{income +}\StringTok{ }\NormalTok{education, }\DataTypeTok{data=}\NormalTok{Duncan)}

\KeywordTok{library}\NormalTok{(texreg)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## Version:  1.36.23
## Date:     2017-03-03
## Author:   Philip Leifeld (University of Glasgow)
## 
## Please cite the JSS article in your publications -- see citation("texreg").
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{texreg}\NormalTok{(}\KeywordTok{list}\NormalTok{(lm1, lm2, lm3), }\DataTypeTok{custom.note =} \StringTok{"Lorem ipsum dolor sit amet, <br>consetetur sadipscing }
\StringTok{       elitr, sed diam. %stars."}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{table}
\begin{center}
\begin{tabular}{l c c c }
\hline
 & Model 1 & Model 2 & Model 3 \\
\hline
(Intercept) & $2.46$       & $0.28$       & $-6.06$      \\
            & $(5.19)$     & $(5.09)$     & $(4.27)$     \\
income      & $1.08^{***}$ &              & $0.60^{***}$ \\
            & $(0.11)$     &              & $(0.12)$     \\
education   &              & $0.90^{***}$ & $0.55^{***}$ \\
            &              & $(0.08)$     & $(0.10)$     \\
\hline
R$^2$       & 0.70         & 0.73         & 0.83         \\
Adj. R$^2$  & 0.69         & 0.72         & 0.82         \\
Num. obs.   & 45           & 45           & 45           \\
RMSE        & 17.40        & 16.69        & 13.37        \\
\hline
\multicolumn{4}{l}{\scriptsize{Lorem ipsum dolor sit amet, <br>consetetur sadipscing 
       elitr, sed diam. $^{***}p<0.001$, $^{**}p<0.01$, $^*p<0.05$.}}
\end{tabular}
\caption{Statistical models}
\label{table:coefficients}
\end{center}
\end{table}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{htmlreg}\NormalTok{(}\KeywordTok{list}\NormalTok{(lm1, lm2, lm3), }\DataTypeTok{custom.note =} \StringTok{"Lorem ipsum dolor sit amet, <br>consetetur sadipscing }
\StringTok{       elitr, sed diam. %stars."}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Statistical models

Model 1

Model 2

Model 3

(Intercept)

2.46

0.28

-6.06

(5.19)

(5.09)

(4.27)

income

1.08***

0.60***

(0.11)

(0.12)

education

0.90***

0.55***

(0.08)

(0.10)

R2

0.70

0.73

0.83

Adj. R2

0.69

0.72

0.82

Num. obs.

45

45

45

RMSE

17.40

16.69

13.37

{Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam.
\emph{\textbf{p \textless{} 0.001, }p \textless{} 0.01, }p \textless{}
0.05.}


\end{document}

Best Answer

Note that you custom note end in a \multicolumn, so you can not use line break comands as \par or \\, but you can use a \parbox:

custom.note = "\\parbox{\\linewidth}{Lorem ipsum dolor sit amet, 
\\\\ consetetur sadipscing    elitr, sed diam. %stars.}"

You can also allow an automatic line break in a narrow \parbox, thus avoiding the excessive width of the last column:

custom.note = "\\parbox{.4\\linewidth}{Lorem ipsum dolor sit amet,
consetetur sadipscing elitr, sed diam. %stars.}"

Option 1: Using `knit_child()` with inline R code

Say your setup is like the following. In the same directory, you have:

`graph.R`

## ---- graph
library(ggplot2)
CarPlot <- ggplot() +
    stat_summary(data= mtcars,
                 aes(x = factor(gear),
                     y = mpg
                 ),
                 fun.y = "mean",
                 geom = "bar"
                 )
CarPlot

`chapter1.Rnw`

Hey, look, a graph (Figure~\ref{fig:graph})!

<<graph, echo=FALSE, message=FALSE, fig.lp='fig:', out.width='.5\\linewidth', fig.align='center', fig.cap="A graph", fig.pos='h!'>>=
@

`main.Rnw`

\documentclass{article}

\begin{document}

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

\Sexpr{knit_child('chapter1.Rnw')}

\end{document}

Then, you can knit the main.Rnw file and compile the resulting .tex file with either pdflatex or xelatex.

The output is:

enter image description here

Note that you can also read the external .R file from the child .Rnw file.

So, the following would have worked just as well.

`chapter1-mod.Rnw`

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

Hey, look, a graph (Figure~\ref{fig:graph})!

<<graph, echo=FALSE, message=FALSE, fig.lp='fig:', out.width='.5\\linewidth', fig.align='center', fig.cap="A graph", fig.pos='h!'>>=
@

`main-mod.Rnw`

\documentclass{article}

\begin{document}

\Sexpr{knit_child('chapter1-mod.Rnw')}

\end{document}

Option 2: Using chunk option `child`

Assuming you have graph.R and chapter1.Rnw from above in the same directory, then your main.Rnw should be:

\documentclass{article}

\begin{document}

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

<<child-demo, child='chapter1.Rnw'>>=
@

\end{document}

Note that you can also read the external .R file from within the child document in this case, too.

So, assuming you had graph.R and chapter1-mod.Rnw from above in the same directory, then your main-mod.Rnw file should be:

\documentclass{article}

\begin{document}

<<child-demo, child='chapter1-mod.Rnw'>>=
@

\end{document}

[Tex/LaTex] Converting TEX to TXT using Pandoc

Short answer: no.

Long answer:

The only ways an automated script can know that the output should contain the word "Proof" are:

1) This knowledge is hardcoded in the script. It knows about the meaning of some latex commands and environments (the via taken by pandoc)

2) It can run tex code and get the output (via taken by t4ht, for example)

The first approach is not flexible enough, since you can load packages which are not known by the script, and which define commands that will be ignored (in addition, your document can define your own commands too).

The second approach can be done via pdflatex followed by some "pdf to text" converter, or via latex followed by dvi2tty, or via tex4ht. In any case, it loses the original tex markup, and then is not appropiate if you want to keep the "code" of the math formulae.

Let's see an example. Consider the following document:

\documentclass{article}
\usepackage{nopageno} % No page numbers
\usepackage{amsthm}

\begin{document}
\begin{proof}
This is a proof
\[
    \sum_{i=0}^\infty x^2
\]
\end{proof}
\end{document}

Running it through standard pdflatex you get:

If you run it through pandoc, you get the following .txt:
```
 This is a proof $$\sum_{i=0}^\infty x^2$$
```
in which you lost the word "Proof", and the final end-of-proof mark, but it keeps the formula markup.
If you run it through pdflatex and then pdftotxt you get:
```
Proof. This is a proof

∞

x2
i=0
```
which keeps the word "Proof", but completly messes the formula

If you run it through latex and then dvi2tty, you get:

Proof. This is a proof
                                1X
                                   x2
                                i=0

                                                                   |___|

Which is closer to the pdf output, but still loses the formula markup.

If you run it through tex4ht you get an HTML version of the document, which can be in turn processed by pandoc to get the following .txt:
```
Proof. This is a proof ∞ ∑ i=0 x2 \_\_
```

As you can see, none of the solutions is satisfactory.

Best Answer

Related Solutions

[Tex/LaTex] Building TeX file from knitr Rnw as child of larger parent TeX file to use R objects and output

Option 1: Using knit_child() with inline R code

graph.R

chapter1.Rnw

main.Rnw

chapter1-mod.Rnw

main-mod.Rnw

Option 2: Using chunk option child