Template for Guide Documents
In stationery: Working Examples for Reproducible Research Documents

##This Invisible Chunk is required in all CRMDA documents
outdir <- paste0("tmpout")
if (!file.exists(outdir)) dir.create(outdir, recursive = TRUE)
knitr::opts_chunk$set(echo=TRUE, comment=NA, fig.path=paste0(outdir, "/p-"))
opts.orig <- options()
par.orig <- par(no.readonly=TRUE)
options(width = 70)

library(stationery)
## If theme directory does not have required images or TeX files
## we need to retrieve them and put them in "theme" directory. 
logos <- c("logoleft.png", "logo-vert.png")
try(getFiles(logos, pkg = "stationery", overwrite = FALSE))
## These theme files should be available already, but if not
themefiles <- c("kutils.css", "guide-template.html")
try(getFiles(themefiles, pkg = "stationery", overwrite = FALSE))
## If you do not have a file after that, 
## the following will manufacture a blank image for a placeholder
if(!file.exists("theme/logoleft.png")){
  blankPNG(file = "theme/logoleft.png", height=200, width=200, messg = "")
}
if(!file.exists("theme/logo-vert.png")){
  blankPNG(file = "theme/logo-vert.png", height=200, width=200, messg = "")
}

Level 1 heading

This is the template file for Markdown documents prepared with R [@RCore] using the CRMDA template. It was probably created by

library(stationery)
initWriteup("rmd2html-guide")

To edit and compile

See the "instructions" file with this document.

HTML Special Features

The instructions document also has a brief reminder about how to specify highlighted call out sections and tabbed sections. Many more details are in the vignette, "HTML_special_features" distributed with the package.

Equations and code chunks can be used too.

Code chunks for HTML documents were the prototype motivation for the development of R markdown. Chunks will work well.

The usage of R code chunks is discussed in the vignette "code chunks". Some examples are included in the instructions file, in the current directory.

R Replication Information

sessionInfo()

if(!is.null(warnings())){
    print("Warnings:")
    warnings()
}

## Don't delete this. It puts the interactive session options
## back the way they were. If this is compiled within a session
## it is vital to do this.
options(opts.orig)
par(par.orig)

Available under Created Commons license 3.0 CC BY