Compiling RMarkdown from a Helper R Script

The problem

The solution

1. A .Rmd file that would actually do all the analysis and generate the compiled report.
2. A second .R script to be used as a config file. Here you’d specify the input data (and potentially other analysis parameters).

 ---
 title: "Analysis Markdown document"
 author: "Stephen Turner"
 date: "August 6, 2015"
 output: html_document
 ---

 This is the Rmarkdown document that runs the analysis.
 Some narrative text goes here. 
 Maybe we'll do some analysis here. The `infile` variable is passed 
 in from the config script. You could pass in other variables too.

 ```{r}
 # check that you defined infile from the config and that 
 # the file actually exists in the current directory
 stopifnot(exists("infile"))

 stopifnot(file.exists(infile))

 # read in the data
 x = read.table(infile)

 # do some stuff, make a plot, etc.
 result = mean(x$value)
 hist(x$value)
 ```

 Here is some conclusion narrative text. Maybe show some notes:

 - Input file used for this report: `r infile`
 - This report was compiled: `r Sys.Date()`
 - The mean of the `value` column is: `r result`

 Also, never forget to show your...

 ```{r}
 sessionInfo()
 ``` 

#-------- define the input filename --------#
infile = "data001.txt"
#----- Now just hit the source button! -----#

# check that the input file actually exists!
stopifnot(file.exists(infile))

# create the output filename
outfile = paste(infile, Sys.Date(), "analysis.html", sep=".")

# compile the document
rmarkdown::render(input="analysis.Rmd", output_file=outfile)