Rework documents to include knitr and knitcitation changes

[trinker]

See:
https://github.com/yihui/knitr/blob/master/vignettes/knit_print.Rmd
http://cran.rstudio.com/web/packages/knitr/vignettes/knit_print.html
https://github.com/cboettig/knitcitations/blob/master/vignettes/tutorial.Rmd

http://rmarkdown.rstudio.com/markdown_document_format.html

[trinker]

First I will change the documents and add the yaml

• vignette.Rmd
• apa6.qual_rmd/doc.Rmd
• apa6.quant_rmd/doc.Rmd
• basic/doc.Rmd
• brew.min_rmd/doc.Rmd
• hw_rmd/doc.Rmd
• wordpress_rmd/doc.Rmd

Then the functions that alter these documents

• new_vignette
• new_report
• qrepo ?

Test the functions/files

• new_vignette
• new_report
• qrepo ?

[trinker]

Figure out what "--csl", "ecology.csl" does in Carl's example README.md. Make sure The vignette template is accurate:

https://github.com/trinker/reports/blob/master/inst/extdata/vign_library/vignette_rmd/doc.Rmd

[trinker]

Very cool this appears to be a way to style references: https://github.com/citation-style-language/styles/blob/master/ecology.csl It would be prudant to remove this from the vignette template in the reprots package. But very cool, very flexible.