---
title: "Add Citations to an RMarkdown Document and Print Bibliography"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{RMarkdown Citations - Alphabetic Style}
  %\VignetteEngine{knitr::knitr}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = TRUE, cache = FALSE}
library(RefManageR)
bib <- ReadBib(system.file("Bib", "biblatexExamples.bib", 
                           package = "RefManageR"), check = FALSE)
BibOptions(check.entries = FALSE, style = "markdown", bib.style = "alphabetic", cite.style = 'alphabetic')
```
  This is an R Markdown document. This is an example of a citation in the text `r Citet(bib, 12, .opts = list(longnamesfirst = FALSE))`. Now we cite in parentheses `r AutoCite(bib, "baez/online", before = "e.g., ")`.  You can change the default options in a setup chunk at the start of the document or at any other point using the <code>BibOptions</code> function or by specifying options as a list in the `.opts` argument to the cite functions.

These are reports `r Citet(bib, bibtype = "Report", .opts = list(hyperlink = "to.doc", super = TRUE))`.  Their hyperlinks go to their entry in the bibliography.
The link for `r AutoCite(bib, "markey")` will take you to the document in a new window; this is the default behaviour, if a link is available (see `?open.BibEntry`). The following citation has no hyperlink `r AutoCite(bib, location = "Uppsala", .opts = list(hyperlink = FALSE))`.  You can also embed plots, for example: 
  
```{r fig.width=7, fig.height=6}
plot(cars)
```
`r NoCite(bib = bib, title = "CTAN")`I've added a reference to CTAN without citing it.  Look at all my Aristotle: `r AutoCite(bib, author = "Aristotle")`.  

```{r fig.width=7, fig.height=6}
plot(cars)
```

Some papers on the arXiv are `r TextCite(bib, eprinttype = "arxiv")`.

**References**

```{r results = "asis", echo = FALSE}
PrintBibliography(bib, .opts = list(check.entries = FALSE))
```

.
