R -e "rmarkdown::render('allTrap_familytree_histogramD.Rmd')"

Run Rmd file from command line

Need to install pandoc first
https://github.com/jgm/pandoc/releases/tag/2.1.1

$R -e "rmarkdown::render('allTrap_familytree_histogramD.Rmd')"

see 

https://github.com/rstudio/rmarkdown/issues/1100

current date in R markdown

date: "May 4 2017 - `r format(Sys.time(), '%d %B, %Y')`"

See
https://stackoverflow.com/questions/23449319/yaml-current-date-in-rmarkdown

R markdown, first try using the default example

I tried R markdown following Roger Peng's youtube example, but I had the following error.

output file: Preview-34861e6a55d2.knit.md
Error: unrecognized fields specified in html_dependency: attachment
Execution halted

Similar problem was online.
http://stackoverflow.com/questions/25790059/r-markdown-error-cant-produce-html-file

My Rstudio is Version 0.98.932

I first installed R3.2.1.
I then installed Rstudio 0.99.447

In Rstudio, I click "Knit-html", this time I was prompt to save a file.
Then

I clicked "Yes", and it updated many packages.

Then, I see the markdown file.

I clicked "open in browser". I can see the html file is in Download folder which I chose.

I then clikced "publish"

I chose "no"


I checked the saved html file. It use javascript and save a lot data within the file itself.