add mentions of quarto vignettes (#150)

Co-authored-by: lshep <lori.shepherd@roswellpark.org>

Author: LiNk-NY

documentation.Rmd

@@ -24,7 +24,7 @@ it is always possible to extend existing classes.
 ## Vignettes {#vignettes}
 
 A vignette demonstrates how to accomplish non-trivial tasks embodying the core
-functionality of your package. There are two common types of vignettes.
+functionality of your package. There are three types of vignettes.
 
 * (Recommended) An *R markdown* vignette is similar to a *Sweave* vignette, but
   uses [markdown](http://daringfireball.net/projects/markdown/) instead of
@@ -34,11 +34,20 @@ functionality of your package. There are two common types of vignettes.
   vignettes][CRAN vigs] for technical details. See the
   `r BiocStyle::Biocpkg("BiocStyle")` package for a convenient way to use common
   macros and a standard _Bioconductor_ style vignette.
-
-* A *Sweave* vignette is an `.Rnw` file that contains $\LaTeX$ and chunks of <i
-  class="fab fa-r-project"></i> code. The  code chunk starts with a line
+  
+* Quarto is a new format for vignettes that uses the
+  [Quarto](https://quarto.org/) system. It is similar to R Markdown but offers
+  more advanced features and flexibility. Similar to R Markdown, Quarto
+  vignettes can be rendered to various formats, including HTML and PDF, and are
+  suitable for multi-language documentation needs. Note that an installation
+  of the `quarto` command line tool is required to build Quarto vignettes.
+
+* A *Sweave* vignette is an `.Rnw` file that contains $\LaTeX$ and chunks of
+  <i class="fab fa-r-project"></i> code. The  code chunk starts with a line
   `<<>>=`, and ends with `@`. Each chunk is evaluated during `R CMD build`,
-  prior to $\LaTeX$ compilation to a PDF document.
+  prior to $\LaTeX$ compilation to a PDF document. Note that this format
+  requires $\LaTeX$ dependencies for rendering that are not be available in
+  standard _Bioconductor_ containers.
 
 A vignette provides reproducibility: the vignette produces the same results as
 copying the corresponding commands into an <i class="fab fa-r-project"></i>
@@ -49,21 +58,20 @@ markdown) undermine the benefit of vignettes and are generally **not allowed**;
 exceptions can be made with proper justification and are at the discretion of
 [_Bioconductor_ reviewers][reviewer-list].
 
-All packages are required to have at least one Rmd or Rnw vignette. Vignettes go
-in the `vignettes/` directory of the package. Vignettes are often used as
-standalone documents, so best practices are to include an informative title, the
-primary author of the vignette, the last modification date of the vignette, and
-a link to the package landing page. We encourage the use of `r
-BiocStyle::Biocpkg("BiocStyle")` for formatting with `html_document` as
-rendering target. Something like the following in the vignette will accomplish
-the above suggestion:
+All packages are required to have at least one Rmd, qmd, or Rnw vignette.
+Vignettes go in the `vignettes/` directory of the package. Vignettes are often
+used as standalone documents, so best practices are to include an informative
+title, the primary author of the vignette, the last modification date of the
+vignette, and a link to the package landing page. We encourage the use of
+`r BiocStyle::Biocpkg("BiocStyle")` with `html_document` as the rendering
+function. For example, in an R Markdown vignette one can use the following
+specification in the yaml front matter:
 
-```
+```yaml
 output:
   BiocStyle::html_document:
     toc: true
     toc_depth: 2
-
 ```
 
 If you want to write more than one vignette, you may want to control
@@ -76,10 +84,10 @@ e.g. using numbers `1-9`, if you have a single digit number of
 vignettes, or `01-99` if you have ten or more vignettes. For example,
 the first vignette could specify in the header:
 
-```
+```yaml
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteIndexEntry{1. Quick start to MyPackage}
+  %\VignetteIndexEntry{1. Quick Start: An Introduction}
   %\VignetteEncoding{UTF-8}
 ```
 
@@ -126,12 +134,11 @@ Include a section with the `SessionInfo()` at the end of the vignette.
 
 ### `vignettes/` directory and intermediate files
 
-Only the source vignette file (`.Rnw` or `.Rmd`) and any necessary static images
-should be in the vignette directory. No intermediate files should be
-present. This include complete processed vignette products as well; the vignette
-should be created through the `R CMD build` of a package. To include other types
-of documentation please use the `inst/doc` or other appropriately named `inst`
-directory.
+Only the source vignette file (`.Rnw`, `.qmd`, or `.Rmd`) and any necessary
+static images should be in the `vignettes/` directory. No intermediate files
+should be present, including vignette products. Vignettes are created through
+by running `R CMD build` on a package. To include other types of documentation
+please use the `inst/doc` or other appropriately named `inst` directory.
 
 ### References