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---+ =knitr= HTML Template | [[http://hbiostat.org/R/Hmisc/examples.html Example html Document]]
Using =knitr= in conjunction with Rmarkdown and RStudio one can produce nice html reports and material for long presentations where pagination into customary slides becomes tedious.  With the RStudio html report format you can also incorporate caching to improve execution time, and include somewhat interactive =plotly= and other Javascript-based graphics.  You can easily produce a floating table of contents.  The usual floating TOC in RStudio puts the TOC in the left margin, which uses a lot of real estate and results in a narrower working space.  Tom Stewart has adapted the html styles to place the floating TOC in the right margin where it collides less often with graphics and text in the report, and the TOC can be clicked off and on.  In addition you can select the heading level the TOC displays using the buttons labeled 1, 2, and 3 under the button that hides the TOC.  The TOC can also be placed in the left margin if you so choose using the =side= argument the the =hidingTOC= function.  The side of the buttons are displayed on can be changed using the =buttonSide= argument.  By default the TOC is displayed on page load.  To hide the TOC on page load set the =hidden= option to =TRUE=.  The depth of the TOC can be adjusted using the =levels= argument.  The =levels= argument value should match the value found in =toc_depth= parameter in the documents yaml metadata header.

Here is a recommended template for reports and presentations.  You'll see in the =hidingTOC= line the text you will click on to expand or contract the TOC (here, "Outline" by default "Table of Contents").  To compile into an html document, use =knit to html= in Rstudio.

<highlight>
--- 
title: "Report Title"
author: "Your Name<br><small>Department of Biostatistics<br>Vanderbilt University School of Medicine</small>"
date: "<small>`r Sys.Date()`</small>"
output:
  html_document:
    toc: yes
    toc_depth: 3
    number_sections: true
    toc_float: 
      collapsed: false
    code_folding: hide
    theme: cerulean
description: "some description ..."
---
```{r setup,echo=FALSE}
require(Hmisc)    # provides knitrSet and other functions
knitrSet(lang='markdown', fig.path='png/', fig.align='left', w=6.5, h=4.5, cache=TRUE)
# If using blogdown: knitrSet(lang='blogdown')

```
`r hidingTOC(buttonLabel="Outline")`
</highlight>

The =hidingTOC= function is in the Hmisc R package.  You can see the source code at https://raw.githubusercontent.com/harrelfe/Hmisc/master/R/hidingTOC.r .

---++ Horizontal Scrolling of R Code
Especially for =blogdown= articles, it is best to activate a horizontal scrollbar for wide code chunks when viewing on a small screen, instead of line-wrapping.  This is simple to do with a small =css= change, as explained [[http://seankross.com/notes/css-for-code][here]]:
<highlight>
pre code {
  overflow: auto;
  word-wrap: normal;
  white-space: pre;
}
</highlight>

---+Tufte html formatting
Another example of report formating is the Tufte style.  An example of this can be seen in the file [[%ATTACHURL%/tufte_rmarkdown.html][tufte_rmarkdown.html]]

Topic attachments
I	Attachment	Action	Size	Date	Who	Comment
css	stewarttoc.css	manage	0.5 K	02 Jan 2018 - 17:43	FrankHarrell	CSS style file for floating TOC in right margin of R html reports
html	tufte_rmarkdown.html	manage	1096.5 K	31 Jan 2019 - 12:37	CharlesDupont	Example of Tufte document formatting applied to a HTML document.

Topic revision: r11 - 25 Jun 2019, FrankHarrell

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