A Template for Two or One-Column Vignettes
In pinp: 'pinp' is not 'PNAS'

Introduction

This pinp is not PNAS template started when the introduction to Rcpp by \cite{PeerJ:Rcpp} was converted into this updated Rcpp Introduction vignette. It is based on the pnas_article template of the wonderful rticles package by \cite{CRAN:rticles}. The conversion from markdown to latex is facilitated by rmarkdown \citep{CRAN:rmarkdown} and knitr \citep{CRAN:knitr}. The underlying LaTeX macros are from pnas.org.

The remainder of the document carries over from the corresponding pnas_article template document. but has been edited and updated to our use case. A few specific tips follow. In general, for fine-tuning some knowledge of LaTeX is helpful.

Author Affiliations

Per common academic best practice, you can include your department, institution, and complete address, with the ZIP/postal code, for each author. Use lower case letters to match authors with institutions, as shown in the example. Authors with an ORCID ID may supply this information at submission.

Document Options

We support several options via the YAML header

Setting a DOI or URL footer, for example for the CRAN package URL, which is placed in the bottom-left footer of the title page and even pages;
Setting a footer label, for example YourPackage Vignette stating your package, which is placed in the bottom-right footer on odd pages;
Setting a free-form author field used on the inside footer;
Optional Draft watermark to be added to each page;
Line of custom text in subtitle (date_subtitle) suitable to give publication info of the draft, e.g. journal name in a post-print;
Document date that appears in the footer can be specified manually using document_date.

References

Here we differ from PNAS and suggest natbib. References will appear in author-year form. Use \citet{}, \citep{}, etc as usual.

We default to the jss.bst style. To switch to a different bibliography style, please use biblio-style: style in the YAML header.

Inline R Code

The PNAS sample included a fixed PNG image here, but this document prefers to show the results and embedding of R code.

library(ggplot2)
ggplot(mtcars, aes(wt, mpg)) +
    geom_point(size=3, aes(colour=factor(cyl))) +
    theme(legend.position="none")

Here we use a standard knitr bloc with explicit options for

figure width and height (fig.width, fig.height), both set to three inches;
whether the code is shown (echo=TRUE); and
the caption (fig.cap) as shown above.

Digital Figures

Markdown, Pandoc and LaTeX support .eps and .pdf files.

Figures and Tables should be labelled and referenced in the standard way using the \label{} and \ref{} commands.

The R examples above show how to insert a column-wide figure. To insert a figure wider than one column, please use the \begin{figure*}...\end{figure*} environment.

One (roundabout) way of doing this is to not actually plot a figure, but to save it in a file as the following segment shows:

library(ggplot2)
p <- ggplot(data = midwest,
            mapping = aes(x = area,
                          fill = state,
                          color = state)) +
    geom_density(alpha = 0.3)
## save to file
suppressMessages(ggsave("densities.pdf", p))

This file is then included via standard LaTeX commands.

\begin{figure} \begin{center} \includegraphics[width=0.66\textwidth, height=3.5in]{densities} \end{center} \caption{Wide ggplot2 figure}\label{fig} \end{figure}

Typeset Code (But Do Not Run It)

We can also just show code.

xx <- faithful[,"eruptions"]
fit <- density(xx)
plot(fit)

This simply used a pandoc bloc started and ended by three backticks, with r as the language choice. Similarly, many other languages can be typeset directly simply by relying on pandoc.

Single column equations

Authors may use 1- or 2-column equations in their article, according to their preference.

To allow an equation to span both columns, options are to use the \begin{figure*}...\end{figure*} environment mentioned above for figures. The \begin{widetext}...\end{widetext} environment as shown in equation \ref{eqn:example} below is deprecated, but \LaTeX commands \onecolumn and \twocolumn work fine.

Please note that this option may run into problems with floats and footnotes, as mentioned in the cuted package documentation. In the case of problems with footnotes, it may be possible to correct the situation using commands \footnotemark and \footnotetext.

\begin{equation} \begin{aligned} (x+y)^3&=(x+y)(x+y)^2\ &=(x+y)(x^2+2xy+y^2) \ &=x^3+3x^2y+3xy^3+x^3. \label{eqn:example} \end{aligned} \end{equation}