Preprint

.Rbuildignore

@@ -16,5 +16,6 @@
 ^NEWS\.md$
 ^CONTRIBUTING\.md$
 ^CODE_OF_CONDUCT\.md$
+^preprint$
 ^doc$
 ^Meta$

R/PHom.R

@@ -28,15 +28,17 @@ validate_PHom <- function(x, error = TRUE) {
   if (!("PHom" %in% class(x) & "data.frame" %in% class(x))) {
     if (error) {
       stop(paste("PHom objects must have classes `PHom` and `data.frame`;",
-                 "paseed value has class =", class(x)))
+                 "paseed value has class =", class(x)),
+           call. = FALSE)
     } else {
       return(FALSE)
     }
   }
   if (ncol(x) != 3) {
     if (error) {
       stop(paste("PHom objects must be data frames with exactly 3 columns;",
-                 "passed object has", ncol(x), "columns."))
+                 "passed object has", ncol(x), "columns."),
+           call. = FALSE)
     } else {
       return(FALSE)
     }
@@ -45,7 +47,8 @@ validate_PHom <- function(x, error = TRUE) {
     if (error) {
       stop(paste("`dimension` column in PHom objects must have class integer;",
                  "`dimension` column in passed object has class =",
-                 class(x$dimension)))
+                 class(x$dimension)),
+           call. = FALSE)
     } else {
       return(FALSE)
     }
@@ -54,7 +57,8 @@ validate_PHom <- function(x, error = TRUE) {
     if (error) {
       stop(paste("`birth` and `death` columns in PHom objects must have",
                  "class integer; respective columns in passed object have",
-                 "classes =", class(x$birth), "and", class(x$death)))
+                 "classes =", class(x$birth), "and", class(x$death)),
+           call. = FALSE)
     } else {
       return(FALSE)
     }
@@ -64,7 +68,8 @@ validate_PHom <- function(x, error = TRUE) {
   if (!all(x$birth < x$death)) {
     if (error) {
       stop(paste("In PHom objects, all births must be before corresponding",
-                 "deaths."))
+                 "deaths."),
+           call. = FALSE)
     } else {
       return(FALSE)
     }
@@ -85,16 +90,19 @@ valid_colval <- function(df, val, val_name) {
 
     if (!(val %in% seq_len(ncol(df)))) {
       stop(paste(val_name, "parameter must be a valid column index for the",
-                 "provided data frame; passed value =", val))
+                 "provided data frame; passed value =", val),
+           call. = FALSE)
     }
   } else if (is.character(val)) {
     if (!(val %in% colnames(df))) {
       stop(paste(val_name, "parameter must be a valid column name for the",
-                 "provided data frame; passed value =", val))
+                 "provided data frame; passed value =", val),
+           call. = FALSE)
     }
   } else {
     stop(paste(val_name, "parameter must either be a valid column name or",
-               "index; passed value =", val))
+               "index; passed value =", val),
+         call. = FALSE)
   }
 }
 

preprint/.gitignore

@@ -0,0 +1,3 @@
+# ignore Rmarkdown output files
+*.pdf
+*.tex

preprint/arxiv.sty

@@ -0,0 +1,256 @@
+\NeedsTeXFormat{LaTeX2e}
+
+\ProcessOptions\relax
+
+% fonts
+\renewcommand{\rmdefault}{ptm}
+\renewcommand{\sfdefault}{phv}
+
+% set page geometry
+\usepackage[verbose=true,letterpaper]{geometry}
+\AtBeginDocument{
+  \newgeometry{
+    textheight=9in,
+    textwidth=6.5in,
+    top=1in,
+    headheight=14pt,
+    headsep=25pt,
+    footskip=30pt
+  }
+}
+
+\widowpenalty=10000
+\clubpenalty=10000
+\flushbottom
+\sloppy
+
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\fancyhf{}
+\pagestyle{fancy}
+\renewcommand{\headrulewidth}{0pt}
+\fancyheadoffset{0pt}
+\rhead{\scshape A preprint - \today}
+\cfoot{\thepage}
+
+
+%Handling Keywords
+\def\keywordname{{\bfseries \emph Keywords}}%
+\def\keywords#1{\par\addvspace\medskipamount{\rightskip=0pt plus1cm
+\def\and{\ifhmode\unskip\nobreak\fi\ $\cdot$
+}\noindent\keywordname\enspace\ignorespaces#1\par}}
+
+% font sizes with reduced leading
+\renewcommand{\normalsize}{%
+  \@setfontsize\normalsize\@xpt\@xipt
+  \abovedisplayskip      7\p@ \@plus 2\p@ \@minus 5\p@
+  \abovedisplayshortskip \z@ \@plus 3\p@
+  \belowdisplayskip      \abovedisplayskip
+  \belowdisplayshortskip 4\p@ \@plus 3\p@ \@minus 3\p@
+}
+\normalsize
+\renewcommand{\small}{%
+  \@setfontsize\small\@ixpt\@xpt
+  \abovedisplayskip      6\p@ \@plus 1.5\p@ \@minus 4\p@
+  \abovedisplayshortskip \z@  \@plus 2\p@
+  \belowdisplayskip      \abovedisplayskip
+  \belowdisplayshortskip 3\p@ \@plus 2\p@   \@minus 2\p@
+}
+\renewcommand{\footnotesize}{\@setfontsize\footnotesize\@ixpt\@xpt}
+\renewcommand{\scriptsize}{\@setfontsize\scriptsize\@viipt\@viiipt}
+\renewcommand{\tiny}{\@setfontsize\tiny\@vipt\@viipt}
+\renewcommand{\large}{\@setfontsize\large\@xiipt{14}}
+\renewcommand{\Large}{\@setfontsize\Large\@xivpt{16}}
+\renewcommand{\LARGE}{\@setfontsize\LARGE\@xviipt{20}}
+\renewcommand{\huge}{\@setfontsize\huge\@xxpt{23}}
+\renewcommand{\Huge}{\@setfontsize\Huge\@xxvpt{28}}
+
+% sections with less space
+\providecommand{\section}{}
+\renewcommand{\section}{%
+  \@startsection{section}{1}{\z@}%
+                {-2.0ex \@plus -0.5ex \@minus -0.2ex}%
+                { 1.5ex \@plus  0.3ex \@minus  0.2ex}%
+                {\large\bf\raggedright}%
+}
+\providecommand{\subsection}{}
+\renewcommand{\subsection}{%
+  \@startsection{subsection}{2}{\z@}%
+                {-1.8ex \@plus -0.5ex \@minus -0.2ex}%
+                { 0.8ex \@plus  0.2ex}%
+                {\normalsize\bf\raggedright}%
+}
+\providecommand{\subsubsection}{}
+\renewcommand{\subsubsection}{%
+  \@startsection{subsubsection}{3}{\z@}%
+                {-1.5ex \@plus -0.5ex \@minus -0.2ex}%
+                { 0.5ex \@plus  0.2ex}%
+                {\normalsize\bf\raggedright}%
+}
+\providecommand{\paragraph}{}
+\renewcommand{\paragraph}{%
+  \@startsection{paragraph}{4}{\z@}%
+                {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+                {-1em}%
+                {\normalsize\bf}%
+}
+\providecommand{\subparagraph}{}
+\renewcommand{\subparagraph}{%
+  \@startsection{subparagraph}{5}{\z@}%
+                {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+                {-1em}%
+                {\normalsize\bf}%
+}
+\providecommand{\subsubsubsection}{}
+\renewcommand{\subsubsubsection}{%
+  \vskip5pt{\noindent\normalsize\rm\raggedright}%
+}
+
+% float placement
+\renewcommand{\topfraction      }{0.85}
+\renewcommand{\bottomfraction   }{0.4}
+\renewcommand{\textfraction     }{0.1}
+\renewcommand{\floatpagefraction}{0.7}
+
+\newlength{\@abovecaptionskip}\setlength{\@abovecaptionskip}{7\p@}
+\newlength{\@belowcaptionskip}\setlength{\@belowcaptionskip}{\z@}
+
+\setlength{\abovecaptionskip}{\@abovecaptionskip}
+\setlength{\belowcaptionskip}{\@belowcaptionskip}
+
+% swap above/belowcaptionskip lengths for tables
+\renewenvironment{table}
+  {\setlength{\abovecaptionskip}{\@belowcaptionskip}%
+   \setlength{\belowcaptionskip}{\@abovecaptionskip}%
+   \@float{table}}
+  {\end@float}
+
+% footnote formatting
+\setlength{\footnotesep }{6.65\p@}
+\setlength{\skip\footins}{9\p@ \@plus 4\p@ \@minus 2\p@}
+\renewcommand{\footnoterule}{\kern-3\p@ \hrule width 12pc \kern 2.6\p@}
+\setcounter{footnote}{0}
+
+% paragraph formatting
+\setlength{\parindent}{\z@}
+\setlength{\parskip  }{5.5\p@}
+
+% list formatting
+\setlength{\topsep       }{4\p@ \@plus 1\p@   \@minus 2\p@}
+\setlength{\partopsep    }{1\p@ \@plus 0.5\p@ \@minus 0.5\p@}
+\setlength{\itemsep      }{2\p@ \@plus 1\p@   \@minus 0.5\p@}
+\setlength{\parsep       }{2\p@ \@plus 1\p@   \@minus 0.5\p@}
+\setlength{\leftmargin   }{3pc}
+\setlength{\leftmargini  }{\leftmargin}
+\setlength{\leftmarginii }{2em}
+\setlength{\leftmarginiii}{1.5em}
+\setlength{\leftmarginiv }{1.0em}
+\setlength{\leftmarginv  }{0.5em}
+\def\@listi  {\leftmargin\leftmargini}
+\def\@listii {\leftmargin\leftmarginii
+              \labelwidth\leftmarginii
+              \advance\labelwidth-\labelsep
+              \topsep  2\p@ \@plus 1\p@    \@minus 0.5\p@
+              \parsep  1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+              \itemsep \parsep}
+\def\@listiii{\leftmargin\leftmarginiii
+              \labelwidth\leftmarginiii
+              \advance\labelwidth-\labelsep
+              \topsep    1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+              \parsep    \z@
+              \partopsep 0.5\p@ \@plus 0\p@ \@minus 0.5\p@
+              \itemsep \topsep}
+\def\@listiv {\leftmargin\leftmarginiv
+              \labelwidth\leftmarginiv
+              \advance\labelwidth-\labelsep}
+\def\@listv  {\leftmargin\leftmarginv
+              \labelwidth\leftmarginv
+              \advance\labelwidth-\labelsep}
+\def\@listvi {\leftmargin\leftmarginvi
+              \labelwidth\leftmarginvi
+              \advance\labelwidth-\labelsep}
+
+% create title
+\providecommand{\maketitle}{}
+\renewcommand{\maketitle}{%
+  \par
+  \begingroup
+    \renewcommand{\thefootnote}{\fnsymbol{footnote}}
+    % for perfect author name centering
+    \renewcommand{\@makefnmark}{\hbox to \z@{$^{\@thefnmark}$\hss}}
+    % The footnote-mark was overlapping the footnote-text,
+    % added the following to fix this problem               (MK)
+    \long\def\@makefntext##1{%
+      \parindent 1em\noindent
+      \hbox to 1.8em{\hss $\m@th ^{\@thefnmark}$}##1
+    }
+    \thispagestyle{empty}
+    \@maketitle
+    \@thanks
+    %\@notice
+  \endgroup
+  \let\maketitle\relax
+  \let\thanks\relax
+}
+
+% rules for title box at top of first page
+\newcommand{\@toptitlebar}{
+  \hrule height 2\p@
+  \vskip 0.25in
+  \vskip -\parskip%
+}
+\newcommand{\@bottomtitlebar}{
+  \vskip 0.29in
+  \vskip -\parskip
+  \hrule height 2\p@
+  \vskip 0.09in%
+}
+
+% create title (includes both anonymized and non-anonymized versions)
+\providecommand{\@maketitle}{}
+\renewcommand{\@maketitle}{%
+  \vbox{%
+    \hsize\textwidth
+    \linewidth\hsize
+    \vskip 0.1in
+    \@toptitlebar
+    \centering
+    {\LARGE\sc \@title\par}
+    \@bottomtitlebar
+    \textsc{A Preprint}\\
+    \vskip 0.1in
+    \def\And{%
+      \end{tabular}\hfil\linebreak[0]\hfil%
+      \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+    }
+    \def\AND{%
+      \end{tabular}\hfil\linebreak[4]\hfil%
+      \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+    }
+    \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\@author\end{tabular}%
+  \vskip 0.4in \@minus 0.1in \center{\today}   \vskip 0.2in
+  }
+}
+
+% add conference notice to bottom of first page
+\newcommand{\ftype@noticebox}{8}
+\newcommand{\@notice}{%
+  % give a bit of extra room back to authors on first page
+  \enlargethispage{2\baselineskip}%
+  \@float{noticebox}[b]%
+    \footnotesize\@noticestring%
+  \end@float%
+}
+
+% abstract styling
+\renewenvironment{abstract}
+{
+  \centerline
+  {\large \bfseries \scshape Abstract}
+  \begin{quote}
+}
+{
+  \end{quote}
+}
+
+\endinput