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Demo.tex
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Demo.tex
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% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
man]{apa6}
\usepackage{amsmath,amssymb}
\usepackage{iftex}
\ifPDFTeX
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
\usepackage{unicode-math} % this also loads fontspec
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
\usepackage{lmodern}
\ifPDFTeX\else
% xetex/luatex font selection
\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
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\usepackage{parskip}
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}{% if KOMA class
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\usepackage{graphicx}
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% Scale images if necessary, so that they will not overflow the page
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% Set default figure placement to htbp
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% turn on hanging indent if param 1 is 1
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{}
\usepackage{calc}
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\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
\ifLuaTeX
\usepackage[bidi=basic]{babel}
\else
\usepackage[bidi=default]{babel}
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% get rid of language-specific shorthands (see #6817):
\let\LanguageShortHands\languageshorthands
\def\languageshorthands#1{}
% Manuscript styling
\usepackage{upgreek}
\captionsetup{font=singlespacing,justification=justified}
% Table formatting
\usepackage{longtable}
\usepackage{lscape}
% \usepackage[counterclockwise]{rotating} % Landscape page setup for large tables
\usepackage{multirow} % Table styling
\usepackage{tabularx} % Control Column width
\usepackage[flushleft]{threeparttable} % Allows for three part tables with a specified notes section
\usepackage{threeparttablex} % Lets threeparttable work with longtable
% Create new environments so endfloat can handle them
% \newenvironment{ltable}
% {\begin{landscape}\centering\begin{threeparttable}}
% {\end{threeparttable}\end{landscape}}
\newenvironment{lltable}{\begin{landscape}\centering\begin{ThreePartTable}}{\end{ThreePartTable}\end{landscape}}
% Enables adjusting longtable caption width to table width
% Solution found at http://golatex.de/longtable-mit-caption-so-breit-wie-die-tabelle-t15767.html
\makeatletter
\newcommand\LastLTentrywidth{1em}
\newlength\longtablewidth
\setlength{\longtablewidth}{1in}
\newcommand{\getlongtablewidth}{\begingroup \ifcsname LT@\roman{LT@tables}\endcsname \global\longtablewidth=0pt \renewcommand{\LT@entry}[2]{\global\advance\longtablewidth by ##2\relax\gdef\LastLTentrywidth{##2}}\@nameuse{LT@\roman{LT@tables}} \fi \endgroup}
% \setlength{\parindent}{0.5in}
% \setlength{\parskip}{0pt plus 0pt minus 0pt}
% Overwrite redefinition of paragraph and subparagraph by the default LaTeX template
% See https://github.com/crsh/papaja/issues/292
\makeatletter
\renewcommand{\paragraph}{\@startsection{paragraph}{4}{\parindent}%
{0\baselineskip \@plus 0.2ex \@minus 0.2ex}%
{-1em}%
{\normalfont\normalsize\bfseries\itshape\typesectitle}}
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{0\baselineskip \@plus 0.2ex \@minus 0.2ex}%
{-\z@\relax}%
{\normalfont\normalsize\itshape\hspace{\parindent}{#1}\textit{\addperi}}{\relax}}
\makeatother
\makeatletter
\usepackage{etoolbox}
\patchcmd{\maketitle}
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{\section*{\normalfont\normalsize\abstractname}}
{}{\typeout{Failed to patch abstract.}}
\patchcmd{\maketitle}
{\section{\protect\normalfont{\@title}}}
{\section*{\protect\normalfont{\@title}}}
{}{\typeout{Failed to patch title.}}
\makeatother
\usepackage{xpatch}
\makeatletter
\xapptocmd\appendix
{\xapptocmd\section
{\addcontentsline{toc}{section}{\appendixname\ifoneappendix\else~\theappendix\fi\\: #1}}
{}{\InnerPatchFailed}%
}
{}{\PatchFailed}
\keywords{R, Teaching, \newline\indent Word count: X}
\DeclareDelayedFloatFlavor{ThreePartTable}{table}
\DeclareDelayedFloatFlavor{lltable}{table}
\DeclareDelayedFloatFlavor*{longtable}{table}
\makeatletter
\renewcommand{\efloat@iwrite}[1]{\immediate\expandafter\protected@write\csname efloat@post#1\endcsname{}}
\makeatother
\usepackage{lineno}
\linenumbers
\usepackage{csquotes}
\ifLuaTeX
\usepackage{selnolig} % disable illegal ligatures
\fi
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\urlstyle{same}
\hypersetup{
pdftitle={A Short Demo of R},
pdfauthor={Hu Chuan-Peng1,2 \& Wen Jia Hui1},
pdflang={en-EN},
pdfkeywords={R, Teaching,},
hidelinks,
pdfcreator={LaTeX via pandoc}}
\title{A Short Demo of R}
\author{Hu Chuan-Peng\textsuperscript{1,2} \& Wen Jia Hui\textsuperscript{1}}
\date{}
\shorttitle{Demo}
\authornote{
This is a demostration of \emph{papaja}.
Enter author note here.
The authors made the following contributions. Hu Chuan-Peng: Conceptualization, Writing - Original Draft Preparation, Writing - Review \& Editing, Supervision; Wen Jia Hui: Writing - Review \& Editing.
Correspondence concerning this article should be addressed to Hu Chuan-Peng, \#122 Ninghai Road, Gulou District, Nanjing, China. E-mail: \href{mailto:[email protected]}{\nolinkurl{[email protected]}}
}
\affiliation{\vspace{0.5cm}\textsuperscript{1} Nanjing Normal University\\\textsuperscript{2} Chinese Open Science Network}
\abstract{%
One or two sentences providing a \textbf{basic introduction} to the field, comprehensible to a scientist in any discipline.
Two to three sentences of \textbf{more detailed background}, comprehensible to scientists in related disciplines.
One sentence clearly stating the \textbf{general problem} being addressed by this particular study.
One sentence summarizing the main result (with the words ``\textbf{here we show}'' or their equivalent).
Two or three sentences explaining what the \textbf{main result} reveals in direct comparison to what was thought to be the case previously, or how the main result adds to previous knowledge.
One or two sentences to put the results into a more \textbf{general context}.
Two or three sentences to provide a \textbf{broader perspective}, readily comprehensible to a scientist in any discipline.
}
\begin{document}
\maketitle
\hypertarget{introduction}{%
\section{Introduction}\label{introduction}}
R is a powerful programming language for statistical analyses and more. We can use R for the whole workflow after getting our raw data, from pre-processing to the final manuscript!
Here we will demonstrate how to use \texttt{papaja} for preparing manuscript in APA 6th style.
\hypertarget{methods}{%
\section{Methods}\label{methods}}
We report how we determined our sample size, all data exclusions (if any), all manipulations, and all measures in the study.
\hypertarget{participants}{%
\subsection{Participants}\label{participants}}
We recruited 44 participants (27 females, age = 20.91 \(\pm\) 2.58). \ldots.
\hypertarget{material}{%
\subsection{Material}\label{material}}
We used \emph{Pyschopy 3} to present stimuli and collect participants' responses. \ldots{}
\hypertarget{procedure}{%
\subsection{Procedure}\label{procedure}}
We follow the procedure of Sui et al (2012)
\hypertarget{data-analysis}{%
\subsection{Data analysis}\label{data-analysis}}
We used R (Version 4.3.1; R Core Team, 2023) and the R-packages \emph{dplyr} (Version 1.1.3; Wickham, François, Henry, Müller, \& Vaughan, 2023), \emph{forcats} (Version 1.0.0; Wickham, 2023), \emph{ggplot2} (Version 3.4.4; Wickham, 2016), \emph{here} (Version 1.0.1; Müller, 2020), \emph{lubridate} (Version 1.9.3; Grolemund \& Wickham, 2011), \emph{papaja} (Version 0.1.2; Aust \& Barth, 2023), \emph{purrr} (Version 1.0.2; Wickham \& Henry, 2023), \emph{readr} (Version 2.1.4; Wickham, Hester, \& Bryan, 2023), \emph{report} (Version 0.5.8; Makowski et al., 2023), \emph{stringr} (Version 1.5.0; Wickham, 2022), \emph{tibble} (Version 3.2.1; Müller \& Wickham, 2023), \emph{tidyr} (Version 1.3.0; Wickham, Vaughan, \& Girlich, 2023), \emph{tidyverse} (Version 2.0.0; Wickham et al., 2019), and \emph{tinylabels} (Version 0.2.4; Barth, 2023) for all our analyses.
\hypertarget{results}{%
\section{Results}\label{results}}
\begin{figure}
\centering
\includegraphics{Demo_files/figure-latex/dprime-1.pdf}
\caption{\label{fig:dprime}\emph{d} prime.}
\end{figure}
See figure \ref{fig:dprime} for \emph{d} prime of the experiment.
Morality (\(F(1, 41) = 4.86\), \(p = .033\), \(\hat{\eta}^2_G = .016\), 90\% CI \([.000, .127]\)) has an effect on \emph{d} prime and there is an interaction bewteen these two variables. \(F(1, 41) = 12.08\), \(p = .001\), \(\hat{\eta}^2_G = .055\), 90\% CI \([.000, .201]\).
\begin{table}[tbp]
\begin{center}
\begin{threeparttable}
\caption{\label{tab:anovaTable}A really beautiful ANOVA table.}
\begin{tabular}{lllllll}
\toprule
Effect & \multicolumn{1}{c}{$\hat{\eta}^2_G$} & \multicolumn{1}{c}{90\% CI} & \multicolumn{1}{c}{$F$} & \multicolumn{1}{c}{$\mathit{df}^{\mathrm{GG}}$} & \multicolumn{1}{c}{$\mathit{df}_{\mathrm{res}}^{\mathrm{GG}}$} & \multicolumn{1}{c}{$p$}\\
\midrule
Identity & .002 & {}[.000, .065] & 0.31 & 1 & 41 & .579\\
Morality & .016 & {}[.000, .127] & 4.86 & 1 & 41 & .033\\
Identity $\times$ Morality & .055 & {}[.000, .201] & 12.08 & 1 & 41 & .001\\
\bottomrule
\addlinespace
\end{tabular}
\begin{tablenotes}[para]
\normalsize{\textit{Note.} Note that the column names contain beautiful mathematical copy: This is because the table has variable labels.}
\end{tablenotes}
\end{threeparttable}
\end{center}
\end{table}
\hypertarget{discussion}{%
\section{Discussion}\label{discussion}}
Here we show R is powerful.
\newpage
\hypertarget{references}{%
\section{References}\label{references}}
\hypertarget{refs}{}
\begin{CSLReferences}{1}{0}
\leavevmode\vadjust pre{\hypertarget{ref-R-papaja}{}}%
Aust, F., \& Barth, M. (2023). \emph{{papaja}: {Prepare} reproducible {APA} journal articles with {R Markdown}}. Retrieved from \url{https://github.com/crsh/papaja}
\leavevmode\vadjust pre{\hypertarget{ref-R-tinylabels}{}}%
Barth, M. (2023). \emph{{tinylabels}: Lightweight variable labels}. Retrieved from \url{https://cran.r-project.org/package=tinylabels}
\leavevmode\vadjust pre{\hypertarget{ref-R-lubridate}{}}%
Grolemund, G., \& Wickham, H. (2011). Dates and times made easy with {lubridate}. \emph{Journal of Statistical Software}, \emph{40}(3), 1--25. Retrieved from \url{https://www.jstatsoft.org/v40/i03/}
\leavevmode\vadjust pre{\hypertarget{ref-R-report}{}}%
Makowski, D., Lüdecke, D., Patil, I., Thériault, R., Ben-Shachar, M. S., \& Wiernik, B. M. (2023). Automated results reporting as a practical tool to improve reproducibility and methodological best practices adoption. \emph{CRAN}. Retrieved from \url{https://easystats.github.io/report/}
\leavevmode\vadjust pre{\hypertarget{ref-R-here}{}}%
Müller, K. (2020). \emph{Here: A simpler way to find your files}. Retrieved from \url{https://CRAN.R-project.org/package=here}
\leavevmode\vadjust pre{\hypertarget{ref-R-tibble}{}}%
Müller, K., \& Wickham, H. (2023). \emph{Tibble: Simple data frames}. Retrieved from \url{https://CRAN.R-project.org/package=tibble}
\leavevmode\vadjust pre{\hypertarget{ref-R-base}{}}%
R Core Team. (2023). \emph{R: A language and environment for statistical computing}. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from \url{https://www.R-project.org/}
\leavevmode\vadjust pre{\hypertarget{ref-R-ggplot2}{}}%
Wickham, H. (2016). \emph{ggplot2: Elegant graphics for data analysis}. Springer-Verlag New York. Retrieved from \url{https://ggplot2.tidyverse.org}
\leavevmode\vadjust pre{\hypertarget{ref-R-stringr}{}}%
Wickham, H. (2022). \emph{Stringr: Simple, consistent wrappers for common string operations}. Retrieved from \url{https://CRAN.R-project.org/package=stringr}
\leavevmode\vadjust pre{\hypertarget{ref-R-forcats}{}}%
Wickham, H. (2023). \emph{Forcats: Tools for working with categorical variables (factors)}. Retrieved from \url{https://CRAN.R-project.org/package=forcats}
\leavevmode\vadjust pre{\hypertarget{ref-R-tidyverse}{}}%
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D., François, R., \ldots{} Yutani, H. (2019). Welcome to the {tidyverse}. \emph{Journal of Open Source Software}, \emph{4}(43), 1686. \url{https://doi.org/10.21105/joss.01686}
\leavevmode\vadjust pre{\hypertarget{ref-R-dplyr}{}}%
Wickham, H., François, R., Henry, L., Müller, K., \& Vaughan, D. (2023). \emph{Dplyr: A grammar of data manipulation}. Retrieved from \url{https://CRAN.R-project.org/package=dplyr}
\leavevmode\vadjust pre{\hypertarget{ref-R-purrr}{}}%
Wickham, H., \& Henry, L. (2023). \emph{Purrr: Functional programming tools}. Retrieved from \url{https://CRAN.R-project.org/package=purrr}
\leavevmode\vadjust pre{\hypertarget{ref-R-readr}{}}%
Wickham, H., Hester, J., \& Bryan, J. (2023). \emph{Readr: Read rectangular text data}. Retrieved from \url{https://CRAN.R-project.org/package=readr}
\leavevmode\vadjust pre{\hypertarget{ref-R-tidyr}{}}%
Wickham, H., Vaughan, D., \& Girlich, M. (2023). \emph{Tidyr: Tidy messy data}. Retrieved from \url{https://CRAN.R-project.org/package=tidyr}
\end{CSLReferences}
\end{document}