---
title: "A Title for Skeleton Template"
subtitle: "A report using R markdown to PDF"
author:
- affiliation: CRMDA
  email: first@ku.edu
  name: First Author
- affiliation: CRMDA
  email: second@ku.edu
  name: Second Author
- affiliation: Institute
  email: third@ku.edu
  name: Third Author
fontsize: 12pt
output:
  pdf_document:
    citation_package: natbib
    fig_caption: true
    highlight: haddock
    keep_tex: false
    latex_engine: pdflatex
    pandoc_args: [--listings]
    template: "theme/report-template.tex"
    includes:
      in_header: "theme/guidePreambleKnitr.tex"
logo: theme/logo.pdf
bibliography: R.bib
header-includes:
- |
  ```{=latex}
  \usepackage{xcolor}
  ```
addr:
  l1: address row 1
  l2: address row 2
  l3: City State Zipcode
  r1: 'Web: http://crmda.ku.edu'
  r2: 'Email: author@ku.edu'
  r3: 'Phone: 123-345-5678'
---

```{r setup, include=FALSE, results='hide'}
##This Invisible Chunk is required in all CRMDA documents
opts.orig <- options()
par.orig <- par(no.readonly = TRUE)
tmpdir <- paste0("tmpout")
if (!dir.exists(tmpdir)) dir.create(tmpdir, recursive = TRUE)
knitr::opts_chunk$set(echo=TRUE, comment=NA, fig.path=paste0(tmpdir, "/p-"))
options(width = 70)
```


```{r ignoremeTexcopy, echo=F, results='hide', warning=FALSE}
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("logo.pdf")
try(getFiles(logos, pkg = "stationery", overwrite = FALSE))
## These theme files should be available already, but if not
themefiles <-c("report-template.tex")
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/logo.pdf")){
  blankPDF(file = "theme/logo.pdf", height=1, width=3.5, messg = "")
}
```

\begin{abstract}
\noindent 
This is an abstract. Please include a terse, yet descriptive
statement here of less than 200 words. It should avoid colloquialisms
and polysyllabic profundities.
\end{abstract}


# Introduction {-}

## Make minimal changes to the top part. {-}

Fill in your name, title, email, tags.  

# Your sections here {-}

Please do use sections and subsections wish brief titles
that are well crafted to guide the reader's eye.

Citation with [@Rcore]

One equation to test

\[
\Sigma_{gt}=\Lambda_{gt}\Psi_{gt}\Lambda'_{gt}+\Theta_{gt}
\]

# `R` Code Chunks {-}

In Reports, raw code chunks displaying input are not generally shown.
Instead, generate valid \LaTeX output or graphic images and include
them. 

If a LaTeX table file has been created from another document,
we do not recommend "cutting and pasting" into this document.
Instead, use "\textbackslash{}input{filename}". 


# Session Info {-}

Session Information is usually not written into a report, but an output file is created by the following pieces.

```{r session, include=FALSE}
zz <- gsub("Rmd", "Rout", knitr::current_input())
capture.output(sessionInfo(), file = zz, append = FALSE)
if (!is.null(warnings())){
    capture.output(warnings(), file = zz, append = TRUE)
}
```

```{r session20, 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)
```
