---
title: "Template for Guide Documents"
subtitle: "Using HTML Output for Guides to be displayed on Web"
author:
 - name: Firstname1 Lastname1
   affiliation: Where Are U
   email: email1@where.edu
 - name: Firstname2 Lastname2
   affiliation: Where Are U
   email: email2@where.edu
advertise: >
   Please  visit [http://crmda.ku.edu/guides](http://crmda.ku.edu/guides) 
keywords: guide, Rmarkdown
abstract: >
    Author, please REMEMBER TO INCLUDE AN ABSTRACT BEFORE FINALIZING THIS DOCUMENT!
checked_by: "First Last"
Note to Authors: please_dont_change_the_next 4 lines!
date: "`r format(Sys.time(), '%b. %e %Y')`"
output:
  stationery::crmda_html_document:
    toc: true
    toc_depth: 2
    highlight: haddock
    theme: default
    citation_package: natbib
    css: theme/kutils.css
    template: theme/guide-template.html
guide_number: 00
bibliography: R.bib
logoleft: theme/logoleft.png
logoright: theme/logo-vert.png
---

```{r ignoremeRsetup, include=FALSE, results='hide'}
##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)
```

```{r ignoremeTexcopy, echo=F, results='hide'}
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.pdf")){
  blankPNG(file = "theme/logoleft.png", height=200, width=200, messg = "")
}
if(!file.exists("theme/logo-vert.pdf")){
  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.



[//]: (All guides must have this as the final stanza)

## R Replication Information
```{r sessionInfo, echo = FALSE}
sessionInfo()
```

```{r warnings, echo = FALSE}
if(!is.null(warnings())){
    print("Warnings:")
    warnings()
}
```

```{r RoptionsRestore, echo=FALSE, include=FALSE}
## 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 <img src="http://crmda.dept.ku.edu/images/cc-3.0.png" alt="CC BY"
style="width: 75px;height: 20px;"/>](http://creativecommons.org/licenses/by/3.0/)

# References
