---
output:
html_document:
toc: true
theme: united
knitrBootstrap::bootstrap_document:
theme.chooser: TRUE
highlight.chooser: TRUE
---
`derfinder` advanced details and usage
======================================
```{r vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE}
## Track time spent on making the vignette
startTime <- Sys.time()
## Bib setup
library('knitcitations')
## Load knitcitations with a clean bibliography
cleanbib()
cite_options(hyperlink = 'to.doc', citation_format = 'text', style = 'html')
# Note links won't show for now due to the following issue
# https://github.com/cboettig/knitcitations/issues/63
## Write bibliography information
write.bibtex(c(knitcitations = citation('knitcitations'),
derfinder = citation('derfinder')[1],
knitrBootstrap = citation('knitrBootstrap'),
knitr = citation('knitr')[3],
rmarkdown = citation('rmarkdown')),
file = 'derfinderRef.bib')
bib <- read.bibtex('derfinderRef.bib')
## Assign short names
names(bib) <- c('knitcitations', 'derfinder', 'knitrBootstrap',
'knitr', 'rmarkdown')
```
# Overview
This is a stub vignette. The real one can be viewed online [here](http://lcolladotor.github.io/derfinder/).
# Reproducibility
Code for creating the vignette
```{r createVignette, eval=FALSE, bootstrap.show.code=FALSE}
## Create the vignette
library('knitrBootstrap')
knitrBootstrapFlag <- packageVersion('knitrBootstrap') < '1.0.0'
if(knitrBootstrapFlag) {
## CRAN version
library('knitrBootstrap')
system.time(knit_bootstrap('derfinderAdvanced.Rmd', chooser=c('boot', 'code'), show_code = TRUE))
unlink('derfinder.md')
} else {
## GitHub version
library('rmarkdown')
system.time(render('derfinderAdvanced.Rmd', 'knitrBootstrap::bootstrap_document'))
}
## Note: if you prefer the knitr version use:
# library('rmarkdown')
# system.time(render('derfinderAdvanced.Rmd', 'html_document'))
## Extract the R code
library('knitr')
knit('derfinderAdvanced.Rmd', tangle = TRUE)
```
Date the vignette was generated.
```{r reproducibility1, echo=FALSE, bootstrap.show.code=FALSE}
## Date the vignette was generated
Sys.time()
```
Wallclock time spent generating the vignette.
```{r reproducibility2, echo=FALSE, bootstrap.show.code=FALSE}
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits=3)
```
`R` session information.
```{r reproducibility3, echo=FALSE, bootstrap.show.code=FALSE, bootstrap.show.message=FALSE}
## Session info
library('devtools')
session_info()
```
# Bibliography
This vignette was generated using `knitrBootstrap` `r citep(bib[['knitrBootstrap']])`
with `knitr` `r citep(bib[['knitr']])` and `rmarkdown` `r citep(bib[['rmarkdown']])` running behind the scenes.
Citations made with `knitcitations` `r citep(bib[['knitcitations']])`.
```{r vignetteBiblio, results='asis', echo=FALSE}
## Print bibliography
bibliography()
```