## ----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') ## ----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) ## ----reproducibility1, echo=FALSE, bootstrap.show.code=FALSE------------- ## Date the vignette was generated Sys.time() ## ----reproducibility2, echo=FALSE, bootstrap.show.code=FALSE------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits=3) ## ----reproducibility3, echo=FALSE, bootstrap.show.code=FALSE, bootstrap.show.message=FALSE---- ## Session info library('devtools') session_info() ## ----vignetteBiblio, results='asis', echo=FALSE-------------------------- ## Print bibliography bibliography()