RStudio's 'Knit HTML' (Ctrl+Shift+K) produces great HTML output from an .Rmd file, that includes author names, table of content, and bibliography/citations as specified in the yaml header.
I have not been able to reproduce the output using scripted R commands, e.g., via Rscript rather than via the RStudio IDE.
How can I get the same output via Rscript? (My end goal is to use travis-ci to build my vignettes the way RStudio would -- because R CMD build doesn't make them in the same way, and they look awful -- and then have travis push to the gh-pages branch of my package repo.)
Example:
---
title: "my package vignette"
author:
- "Author1"
- "Author2"
date: "`r format(Sys.Date(), format='%B %d %Y')`"
output:
html_document:
number_sections: yes
self_contained: yes
toc: yes
vignette: >
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{my package vignette}
%\VignetteKeyword{keyword1, keyword2}
%\usepackage[utf8]{inputenc}
references:
- id: fenner2012a
title: One-click science marketing
author:
- family: Fenner
given: Martin
container-title: Nature Materials
volume: 11
URL: 'http://dx.doi.org/10.1038/nmat3283'
DOI: 10.1038/nmat3283
issue: 4
publisher: Nature Publishing Group
page: 261-263
type: article-journal
issued:
year: 2012
month: 3
---
# Section 1
Lorem ipsum ...
# Section 2
Quisque dignissim ... I'll cite @fenner2012a here for fun.
# References
