In rmlane/bscContentHelpers: Templates and Utility Functions for BSC Content

knitr::opts_chunk$set(
    echo      = FALSE, 
    eval      = TRUE, 

    # output settings for PDFs
    fig.pos   = "H", 
    out.extra = "", 
    fig.show  = 'hold', 
    fig.align = 'center'
    )

# image settings for html and pdf
# [only applies to images inserted with knitr::include_graphics()]

if(knitr::is_html_output()) {
    knitr::opts_chunk$set(dpi = 72)

    } else if(knitr::is_latex_output()) {
        knitr::opts_chunk$set(out.width = "100%")
        }

This is some introductory text. It will appear above the table of contents.

# insert a page TOC at the top of the page
blogdown::shortcode_html("toc")

Note About Headers

When this file is rendered as a webpage, the title will be assigned an <H1> html tag. It's a good idea to make the header hierarchy for page content start with level 2 (i.e., start the line with ##) so section headers don't compete with the page title for importance.

Overview

Update this template with your custom content. Then create a formatted output document by pressing the Knit button in or using the Shift + Ctrl + K shortcut in R Studio.

A new output directory will be created, containing a copy of this .Rmd file (renamed index.Rmd) and subfolders for supporting documents.

YAML Header Options

Web-specific options

TODO: expand

slug, weight, type, tags

Knit Function

The default knit function for this document is bscContentHelpers::knit_for_web. When you knit the document, a few things will happen:

• A "page bundle" (an output folder with supporting files) will be created, with a name corresponding to this document's title. All files in the current folder will be included in the page bundle.
  • In the page bundle, this .Rmd source file will be renamed index.Rmd.
  • Unless you set include_pdf to FALSE in the YAML header, a PDF version of this document will be generated and put in the page bundle's files/ subdirectory.
  • Any additional attachments named in the YAML header will also be copied to files/.
  • A code chunk will be added to the end of the document to insert links to all attachments in files/.

The page bundle will be suitable for inclusion in the BSC site. (Note that you'll still need to preview and build the page locally before it can go live on the site. See the site repo and README for more.)

Other Output Formats

If you'd rather just output a static document (like a PDF), you're better off using the Article template.

Other Document Options

You can set some additional properties in the header, such as output file name and location. If you don't customize these, defaults will be used. See the README for more.

Shortcodes

Some code should just be rendered if the output is HTML (e.g., a web page). Conditionally execute code chunks by setting eval=knitr::is_html_output().

Shortcodes are special types of code chunks specifically for webpages built with Hugo.

• More from blogdown
• More from geekdocs

Some useful shortcodes:

blogdown::shortcode_open("hint", "warning")

Only evaluate shortcodes if output is html. Suppress for pdf.

blogdown::shortcode_close("hint")

Markdown

This document is written in R Markdown.

Some common markdown syntax is demonstrated below. More information is available from RStudio, among many other places.

Text Formatting

Text can easily be made italic or bold or ~~strikethrough~~ or ~subscript~ or ^superscript^.

Lists

You can make unordered lists:

• An item
• Another item

You can also make ordered lists:

1. Something
2. A second thing
3. Note that the numbers don't need to be correct. R Markdown will take care of numbering the list during rendering.

Code Chunks

Embed R code and results via code chunks. You can decide whether to print the code, the results, and any messages or warnings.

mean_speed <- mean(cars$speed)
mean_speed

Objects in the current environment are accessible via inline code. For example, the mean speed of the cars dataset is r mean_speed.

If you want to print the code verbatim without running it, you can do that by adjusting the chunk options:

min_speed <- min(cars$speed)
min_speed

And if you want to run code without printing it, you can do that too.

max_speed <- max(cars$speed)
max_speed

The maximum speed is r max_speed.

Images

Save image files in the images/ subdirectory. Insert them into the document like this:

knitr::include_graphics("path/to/image.png")

Equations

Equations can be easily inserted with standard LaTeX syntax. Inline: $y_i = \beta_0 + \beta_1x_i + \varepsilon_i$

Standalone:

$$y_i = \beta_0 + \beta_1x_i + \varepsilon_i$$

Figures and Tables

Print a formatted table with knitr::kable() and refer to it as Table \@ref(tab:cars-table):

knitr::kable(
  head(cars),
  caption = "A table with some car data." #,longtable = TRUE
  )

Tip: to allow tables to break across PDF pages, pass kable(..., longtable = TRUE).

Generate a plot and refer to it as Figure \@ref(fig:cars-figure):

plot(cars)

Citations

Citations are stored as BibTeX entries in references.bib. They can be referenced inline by BibTeX id [@rmarkdown].

Footnotes

Insert a footnote anywhere.[^my-note]

[^my-note]: Citations and footnotes will be formatted automatically when you render the document.

rmlane/bscContentHelpers documentation built on Jan. 30, 2024, 9:43 a.m.