The pinp is not PNAS template extends and reworks the pnas_article template from the wonderful rticles package. This vignette aims to list all the available option in order to provide both a reference documentation, and a simple introduction. The source of this vignette is of course included in the package itself.
author
Fields name
and affiliation
must be given. The latter can be a
single-letter index referring to the address field described in the
next paragraph.
address
Fields code
(referring to the index from affiliation
) and
address
must be given. The latter is free-form, and may include
\url{}
and other LaTeX macros.
lead_author_surnames
A free-form field usable for either a simple "Author et al", or a simple text field listing two or more authors. This field is not post-processed.
doi_footer
A free-form URL for a doi reference for a publication, or a canonical URL for a software package or repository. These are typeset as actual URLs and resolve their links from the pdf document following standard LaTeX practice.
abstract
A short free-form abstract can be used to inform the reader of the essence of the subsequent document.
acknowledgements
An optional free-form text which will be typset at the very end of the document right before the (optional also) references.
keywords
An optional list (entered as a YAML list following -
marks) which will be typeset as a list of alternatives separated by vertical pipe symbols.
fontsize
Default it 9pt, also supported are 10pt, 11pt and 12pt which may make sense in one-column mode.
one_column
An optional override (using value true
) for the default two-column
layout. Useful for initial stages of a document, as well as for
documents with wide-format tables and figures.
lineno
An optional selection (via value true
) of line numbers,
selectable only if one_column: true
is set. Currently typesets
number on both the left and right-hand side which seems in error.
one_sided
An optional selection (via value true
) of one-sided rather than
two-sided output. This should probably alter the footnote but does not
currently do so.
numbersections
An optional selection (via value true
) for overriding the default
unnumbered section headers. Useful if you need to refer to sections by number.
secnumdepth
An optional selection (via values 1, 2, 3, ...) of section numbering depth,
selectable only if numbersections: true
is set. Useful if you only want
to number sections and subsections but not subsubsections and so on.
skip_final_break
An optional selection (via value true
) that avoids inserting a \pnasbreak
at the end of the document. This is useful when dealing with float issues that
may appear at the end of documents with acknowledgements and bibliographies.
bibliography
A field for an optional selection of a Bibtex input file, extension
can be omitted. Alternative, bibliographic information may also be
included directly as a thebibliography
environment by including the
content of the generated bbl
file. The after_body
include of the
YAML header can also be used.
watermark
An optional selection of a 'Draft' watermark drawn across the center
of the page (using value true
). Note that figures may be plotted
above the watermark.
footer_contents
An character value delimited by quotes for something like "mypackage Vignette" which will be shown in the footer.
date_subtitle
An optional free-form text string. Could be used, for example, to mention the bibliographic info in a post-print. If not specified, defaults to "This version was compiled on {current date}"
document_date
An optional free-form text string designed to specify the date of the document. It can be useful for example to specify the exact date of the publication in a post-print. If not specified, defaults to the current date.
The knitr package \citep{CRAN:knitr} is also available to both typeset code, typically in R or one of the other supported engines. Knitr segments used three backticks (just like Pandoc described below) followed by curly brace sgement listing first the desired engine, and then the selected display options. Output from the code can also be shown, and a myriad of options permit many variants.
a <- 2 + 2 a
Output from such code blocks is also shown in a framed and shaded box. Code segments containing plots producing figures results in these figures being automatically inlined:
set.seed(42) par(mar=c(3,3,3,0)) plot(cumsum(rnorm(100)), type='l', main="Up and and away")
The easiest way to typeset code is to simply open three backticks followed by the name of one of the numerous built-in pandoc parsers, i.e., \verb|```c| to typeset in the C languags.
/* this is a C function example */ int doubleMe(int x) { return x + x; }
Pandoc segments are highlighted as usual, and per a convention in this template also shown in a framed and slightly shaded box as seen here and above.
Another example from Python:
# A Python example def printSomething(str): "This prints the string passed in" print str
All standard LaTeX environment are directly usable if needed, including of course all mathematical environments and symbols such as, say, the greek lettering: $\alpha$, $\beta$, $\gamma$, and so on.
The following is set as usual via the displaymath
environment:
\begin{displaymath} a^2 = b^2 + c^2 \end{displaymath}
Figure can span two columns (when the default two-column mode is used)
by using a (LaTeX) \begin{figure*} ... \end{figure*\it}
environment, .
Figures will then be floats in the LaTeX sense and place at the top
or bottom of the page. An example is given by the skeleton document
of the package. Similarly, \begin{figure*} ... \end{figure*}
could
be used around a wide table structure.
The \begin{widetext} ... \end{widetext}
environment can be used to
break text from two-column mode to one-column mode and back. As of the
2018 release of the underlying PNAS macros, this feature is deprecated
upstream. But both the figure*
and table*
environments work, as
does relying on \LaTeX commands \onecolumn
and \twocolumn
.
The rmarkdown site by RStudio is very comprehensive and can answer many questions pertaining to Markdown processing in R using the rmarkdown package.
Ultimately, this style uses LaTeX to produce the pdf output. The tex StackExchange can be very helpful for specific LaTeX questions.
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