pass parameters and run a rmd report in a "clean environment"

create_report.R

# this function will run a rmd report in a "clean environment", which means it 
# ignores what's in the global environment and what packages have been attached.
# It can be fed adhoc parameters however.
#
# "clean environment" is between quotes because loaded namespaces in the 
# original environment CAN influence the report, and the rmd rendering CAN alter
# the loaded namespaces.
#
# In practice this should not be an issue in most cases but let it be said that
# the only known way to be sure about the reproduciblity of a report is to knit
# it in a new session.
#
# As a last note, the following overwrites library locally and uses attach
# (2 times!), you've been warned.
# 
# Read on below for an example (result : https://jsfiddle.net/cLya01qu/ )
create_report <- function(.rmd, .html, ..., unload = FALSE){
  # get loaded packages "package:*" strings
  packages <- grep("^package:",search()[1:(match("package:stats",search())-1)],value = TRUE)
  
  # cleanup and save search path
  sapply(packages, detach, character.only = TRUE)
  search_  <- search()
  
  # set back to normal in the end
  on.exit({
    # remove whatever was attached during the rendering
    sapply(setdiff(search(),search_),detach, character.only = TRUE)
    # reattach the original packages
    sapply(rev(gsub("^package:","",packages)), library, character.only=TRUE)
  })

  # define a new library function locally so our rmd attaches packages after
  # our attached environment
  library2 <- function(...) {
    dots <- alist(...)
    if("pos" %in% names(dots)) dots$pos <- dots$pos + 1
    else dots$pos <- 3
    do.call(base::library,dots)
  }
  
  attach(list(library = library2),pos = 2,name = "library_env")
  attach(list(...), pos = 2,name = "render_env")

  rmarkdown::render(.rmd, output_format = "html_document",
         output_file = .html,
         envir = as.environment("render_env"))
  detach("render_env")
  detach("library_env")
}

######################################
#              EXAMPLE               #
######################################

rmd_input   <- tempfile(fileext = ".Rmd")
html_output <-tempfile(fileext = ".html")

# create the rmd file
# you must correct the indentation if you copy this in R Studio!
# (Alt + select and suppr is your friend!)
cat(
'---
title: "Parametric report"
output: html_document
---

```{r}
library("data.table")
search() # only data.table, no tidyverse package!
ls()     # clean workspace, contains only fed parameters
x <- "don\'t you ignore me!"
for (obj in c("x","y","z","as_tibble","as.data.table")){
  if(is.null(get0(obj)))
    print(paste(obj,"was NOT found"))
  else
    print(paste(obj,"was found"))
}
ggplot2::qplot(0,0, geom="text",
label="I can also call use \'fun::pkg\' notation for unattached packages")
```',file = rmd_input)

# if you want to open it:
# file.edit(rmd_input)

# let's populate our search path
library(tidyverse)
library(rlang)
search()
#  [1] ".GlobalEnv"        "package:rlang"     "package:forcats"   "package:stringr"  
#  [5] "package:dplyr"     "package:purrr"     "package:readr"     "package:tidyr"    
#  [9] "package:tibble"    "package:ggplot2"   "package:tidyverse" "tools:rstudio"    
# [13] "package:stats"     "package:graphics"  "package:grDevices" "package:utils"    
# [17] "package:datasets"  "package:methods"   "Autoloads"         "package:base"     

# now let's populate the workspace
y <- "I will be fed to the report"
z <- "I won't"

# and now create a report from `y` only :
create_report(rmd_input, html_output, y = y)

# and open the result : works on windows, not sure on other systems!
shell(html_output)

# we get our clean path back
search()

# cleanup
# file.remove(rmd_input)
# file.remove(html_output)