Automate PDF Reports in R - r

Question

I have a .CSV file that includes an ID column and several text columns (title of story, content of story) and columns for a multiple choice questions (each question in a different column). Also, there are columns for a numerical variable (ternary plots).
Here is a screen shot of the CSV file:
CSV File
Now what I'm trying to do is to automatically generate multiple PDF reports for each ID number (generate a unique report for each individual person). With different values in the report depending on the ID column in the CSV.
I thought the best way to do that in R was to create a RMarkdown file and use parameters to make the values of the report match the ID number values.
Here is my code for the RMarkdown file:
---
title: "`r params$new_title`"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
pdf_document:
latex_engine: xelatex
html_document:
df_print: paged
header-includes:
\usepackage{fontspec}
\usepackage{fancyhdr}
mainfont: Arial
params:
id:
label: ID
value: 1
input: select
choices:
- 1
- 2
- 3
- 4
- 5
new_title: "My Title!"
---
library(tidyverse)
library(ggtern)
library(ggplot2)
library(readr)
library(lubridate)
library(magrittr)
library(rmarkdown)
knitr::opts_chunk$set(echo = FALSE)
data <- readr::read_csv("dummy.csv")
data_id <- data %>%
filter(id == v)
**Your title:** `r data_id$title`
**Your micro-narrative:** `r data_id$narrative`
Now the code is working, but the formatting in the generated report is not how I want it.
If the same ID number has multiple entries for story title and story content, the values are displayed next to each other. What I want is this:
Story #1 title:
Story #1 content:
Story #2 title:
Story #2 content:
and NOT:
Title: story#1 title, story#2 title, etc...
Content: story#1, story#2, etc...
To automatically generate multiple reports with one click, I created a loop. Here is the code:
require(rmarkdown)
data = read_csv("dummy.csv")
slices = unique(data$id)
for (v in slices){
render("~/Desktop/My_L3/report.Rmd", output_file = paste0("~/Desktop/report_", v, ".pdf"),
params=list(new_title=paste("Quarterly Report -", v)))
}
The loop is working and I was able to generate multiple PDFs by just running this code.
Is this the easiest way to do it? Any other way you're aware of?
And lastly, how do I include the multiple choice questions in the RMarkdown file?
For example, if a certain ID number has 3 choices selected (three 1s in the CSV) how do I display the result as the following:
You selected the following choices: bananas, apples, oranges
I would really appreciate your help as I'm an R noob and still learning a lot of stuff.

Answer 1

#badi congrats! For a newcomer to R you managed already quite a steep hill.
I hope the following will help you moving further:
(I) observation: use of rmarkdown::render(... , params = list(...))
You can pass multiple variables and objects as params to your "report" Rmd.
Thus, when you have lengthy preparatory steps, you can load your data, prepare it, and filter it with the loop you use to call rmarkdown::render().
E.g. inside your for loop you could do something like df <- data %>% filter(id == v) and then pass df as (one of the) params, e.g. rmarkdown::render(... , params = list(new_title=paste("Quarterly Report -", v)), data = df)
Then define a params for the dataframe. I recommend to "load" a dummy object/df, e.g.
...
params:
id ...
data: !mtcars # dummy object/df - do not forget the ! mark
(II) printing dynamic and static text
There are different ways to achieve this. For your example, it looks like you are looking for something relatively well-formatted that can be constructed from your table columns.
For this sprintf() is your friend. I abbreviated your example with a lighter dataframe.
I print this in the beginning of the document/pdf output.
For this you have to set the chunk parameter results = "as-is" and wrap the sprintf() call into a cat() to allow the template formatting and block R/Rmd from adding other output format stuff (e.g. the ## you can see when I print the table above).
The choices you can combine with a paste() call. Of course this can be done with varying levels of sophistication that I leave to you to explore.
I keep the 1 and NA coding. You can replace these with what you think is appropriate (ifelse/case_when, or complex(er) string substitute operations.
To prepare the list of choices, I just paste everything together:
df <- params$data %>%
mutate(choice_text = paste(choice1, choice2, choice3, sep = ","))
The following code-chunk defines the static/dynamic text template for sprintf() and we iterate over the rows of the data dataframe
# to programmatically print text sprintf()
# allows to combine static and dynamic text
# first define a template how your section looks like
# %s points to a string - not used here by %f caters for (float)numbers
template <- "
## Title %s
With content: %s.
\n You selected the following choices: %s
" # end of your "dynamic" text template
# recall to add an empty line for spacing
# you can force a new line for text entries with \n
# iterate over the input data frame
for (i in seq(nrow(df))) {
current <- df[i, ]
cat(sprintf(template, current$title, current$content, current$choice_text))
}
With the adequately set-up pdf template, you will get the following.
Note: My report breaks over to a 2nd page, I only show the first page here.