A demonstration of the \LaTeX class file for Statistical Methods in Medical Research with Rmarkdown

In rticles: Article Formats for R Markdown

The Article Header Information

YAML header:

output:
  rticles::sim_article:
    keep_tex: TRUE

Configure the YAML header including the following elements:

• title: Title

• runninghead: Author last names, use et al. if there are three or more authors.

• author: List of author(s) containing name and num

• corrauth: Corresponding author's name and address.

• email: Correspondence email

• abstract: Limited to 200 words

• keywords: Keywords for the article

• bibliography: BibTeX .bib file

• bibliographystyle: sageh or sagev

• classoption: options of the sagej class

Remarks

1. bibliographystyle

2. classoption

3. Keywords are separated by commas.

The Body of the Article

Mathematics

Use mathematics in Rmarkdown as usual.

Figures and Tables

Figures are supported from R code:

```r", out.width='100%'} x = rnorm(10) y = rnorm(10) plot(x, y)

...and can be referenced (Figure \ref{fig:plot}) by including the `\\label{}` tag in the `fig.cap` attribute of the R chunk: `fig.cap = "Fancy Caption\\label{fig:plot}"`. It is a quirky hack at the moment, see [here](https://github.com/yihui/knitr/issues/323).

Analogously, use Rmarkdown to produce tables as usual:

```r
if (!require("xtable")) install.packages("xtable")
xt <- xtable(head(cars), caption = "A table", label = "tab:table")
print(xt, comment = FALSE)

Referenced via \ref{tab:table}. You can also use the YAML option header-includes to includes custom \LaTeX packages for tables (keep in mind that pandoc uses longtables by default, and it is hardcoded; some things may require including the package longtable). E.g., using ctable:

header-includes:
- \usepackage{ctable}

Then, just write straight-up \LaTeX code and reference is as usual (\ref{tab:ctable}):

\ctable[cap = {Short caption},
        caption = {A caption for this table.},
        label={tab:ctable},]
        {cc}
        {
        \tnote[$\ast$]{Footnote 1}
        \tnote[$\dagger$]{Other footnote}
        \tnote[b]{Mistakes are possible.}
        }{
        \FL
        COL 1\tmark[a] & COL 2\tmark[$\ast$]
        \ML
        6.92\tmark[$\dagger$] & 0.09781 \\
        6.93\tmark[$\dagger$] & 0.09901 \\
        97 & 2000
        \LL
}

It is also possible to set the YAML option longtable: true and use markdown tables (or the knitr::kable function): knitr::kable(head(cars)) produces the same table as the xtable example presented before.

Cross-referencing

The use of the Rmarkdown equivalent of the \LaTeX cross-reference system for figures, tables, equations, etc., is encouraged (using [@<name>], equivalent of \ref{<name>} and \label{<name>}). That works well for citations in Rmarkdown, not so well for figures and tables. In that case, it is possible to revert to standard \LaTeX syntax.

Double Spacing

If you need to double space your document for submission please use the doublespace option in the header.

Bibliography

Link a .bib document via the YAML header, and bibliography will be printed at the very end (as usual). The default bibliography style is provided by Wiley as in WileyNJD-AMA.bst, do not delete that file.

Use the Rmarkdown equivalent of the \LaTeX citation system using [@<name>]. Example: [@Taylor1937], [@Knupp1999; @Kamm2000].

To include all citation from the .bib file, add \nocite{*} before the end of the document.

Further information

All \LaTeX enviroments supported by the main template are supported here as well; see the .tex sample file here for more details and example.

rticles documentation built on May 31, 2023, 6:12 p.m.