[Minimal Function to generate HTML report using RMarkdown] #R

minimal_html_report.R

## This is a minimal example to show how you can create a
## function that generates HTML reports using RMarkdown.
## 
## This uses a list-pmap workflow so you can input lists
## as arguments and dynamically produce a RMarkdown that
## is only limited by the length of your lists.
##
## The example below outputs a table and two plots from
## `iris`.

#### Load packages ####
library(tidyverse)

#### Generate list of outputs ####

## 1. A summary table
summary_table <-
  iris %>%
  group_by(Species) %>%
  summarise_all(~mean(.))

## 2. Plot of Sepal variables
sepal_plot <-
  iris %>%
  ggplot(aes(x = Sepal.Length,
             y = Sepal.Width,
             colour = Species)) +
  geom_point()

## 3. Plot of Petal variables
petal_plot <-
  iris %>%
  ggplot(aes(x = Petal.Length,
             y = Petal.Width,
             colour = Species)) +
  geom_point()

## Combine all outputs into a list of 3 objects
output_list <- 
  list(summary_table,
       sepal_plot,
       petal_plot)

#### Function to generate chunk strings ####
## This is only used as a supporting function
## Not used directly
#'
#' @param level Numeric value to specify the header level of the chunk.
#' @param title Character string to specify the title of the chunk.
#' @param echo Logical value to specify whether to display code.
#' @param object Character string to specify name of the object to show.
generate_chunks <- function(level = 3, title, echo = FALSE, object){
  
  level_hash <- paste(rep('#', level), collapse = "")
  
  obj <- c(paste(level_hash, title),
           paste0('```{r, echo=', echo, '}'),
           object,
           '```',
           ' ')
  
  return(obj)
}

#### `minimal_html2()`` - with list-pmap workflow ####
##
## This the main function for creating a HTML document.
## 
## NOTE THAT `outputs`, `titles`, `echos`, and `levels` must have the same length
#' @param title Character string to specify the title of the chunk.
#' @param filename File name to be used in the exported HTML.
#' @param outputs A list of outputs to be added to the HTML report.
#' @param titles A list/vector of character strings to specify the title of the chunks.
#' @param echos A list/vector of logical values to specify whether to display code.
#' @param levels A list/vector of numeric value to specify the header level of the chunk.
minimal_html2 <- function(title = "My minimal HTML generator",
                         filename = "minimal_html",
                         outputs = output_list,
                         titles,
                         echos,
                         levels){
  
  
  
  ## Title of document
  title_chr <- paste0('title: \"', title, '\"')
  
  
  ## chunk loopage
  ## merged to create `chunk_merged`
  
  chunk_merged <-
    list(output = outputs,
         title = titles,
         echo = echos,
         level = levels,
         id = seq(1, length(outputs))) %>%
    purrr::pmap(function(output, title, echo, level, id){
      
      generate_chunks(level = level,
                      title = title,
                      echo = echo,
                      object = paste0("outputs[[", id, "]]"))
      
    }) %>%
    reduce(c)
  
  
  ## markdown object
  markobj <- c('---',
               title_chr <- paste0('title: \"', title, '\"'),
               'output: ',
               '  html_document:',
               '    theme: united',
               '    toc: true',
               '    toc_float:',
               '      collapsed: false',
               '      smooth_scroll: true',
               
               '---',
               '',
               '',
               chunk_merged)
  
  writeLines(markobj, paste0(filename, ".Rmd"))
  rmarkdown::render(paste0(filename, ".Rmd"))
  
  ## Load in browser
  utils::browseURL(paste0(filename, ".html")) 
  
  ## Deletes specified files
  unlink(c(paste0(filename, ".Rmd"),
           paste0(filename, ".md")))
  
  
}


#### Run example ####

minimal_html2(title = "My minimal HTML generator",
              filename = "minimal_html",
              outputs = output_list,
              titles = c("Summary Table", "Sepal Plot", "Petal Plot"),
              echos = rep(FALSE, 3),
              levels = rep(3, 3))