setup.APS.knitr: Set up knitr documents to contain AnalysisPageServer data...

In apomatix/AnalysisPageServer: A framework for sharing interactive data and plots from R through the web

Description

If you want to embed APS data sets within a knitr document then this function should be called at the top of the document like this:

Usage

setup.APS.knitr(outdir, include.css = system.file("AnalysisPageServer.css",
  package = "AnalysisPageServer"), include.toc = TRUE,
  libbase.prefix = get.APS.libbase.prefix(), quiet = TRUE)

Arguments

outdir	Output directory to which front end files should be written. Default: see details.
include.css	Paths to CSS files to include. See details.
include.toc	Boolean, default TRUE. Should I include a table of contents?
libbase.prefix	Passed to custom.html.headers. Default: get.APS.libbase.prefix().
quiet	Boolean, default TRUE. Set to FALSE to turn on some diagnostic messages

Details

```{r echo = FALSE} AnalysisPageServer::setup.knitr() ```

Calling this function has the following effects:

1. The first effect is a heinous crime. It looks up the call stack to see if you are in the middle of a buildVignettes call. If so then it sets clean = FALSE for that call. The reason for this is that for the document to work it will need a bunch of auxiliary files like .css and .js, and if clean = TRUE then these files won't be left and your data sets will not show at all. During R CMD build buildVignettes is explicitly called with clean = TRUE so this is the only way I could figure out how to turn it off. If it can't find buildVignettes in the call stack then nothing special happens. This would be the case if you are just calling knit2html yourself.

2. The next effect is to copy all the front end files to the output directory. The default output directory is also kind of heinous. The files need to be next to the output file. So the function again looks up the call stack to find the knit2html call, then grabs the name of the output file from there and uses its directory as outdir. If it can't find a knit2html call then it throws an error.

   The output directory is saved with a call to the private function set.APS.outdir. This is then read back by embed.APS.dataset so that the data sets get written to the write place. You could add a reset.APS.outdir() call in a chunk at the bottom of your knitr document.

3. Any files in include.css are copied to the output directory and included as CSS. The default is a default stylesheet that will make your reports look like the vignettes.

Finally it returns the html headers as a "knit_asis" object to be included in your document. See custom.html.headers.

Value

HTML headers as knit_asis objects.

Author(s)

Brad Friedman

Examples

message("See vignette embedding.html")

apomatix/AnalysisPageServer documentation built on May 26, 2019, 11:36 a.m.