Parameterized reports in RMarkdown - How to ask for parameters once? - r

Question

I am currently trying to utilize parameterized reports to allow users to input a dataset (and a few more variables of interest) that will then be fed into an R script that performs and outputs a variety of analyses. These datasets will have information on multiple subjects, and the goal is to produce one report for each subject within the dataset. Thus, I utilize a for loop that loops through the Usernames within the dataset (called map). I then input a .Rmd file which is responsible for the bulk of the analysis. The for loop essentially refers to this .Rmd file for the 50 or so subjects, and outputs the 50 or so reports.
for (id in unique(map$UserName)){
# bunch of code for processing
render(input = "../lib/scripthtml.Rmd",output_file = paste0('report.',
id, '.html'),"html_document",
output_dir = "Script_output", params = "ask") }
What I am currently trying to do is I am trying to utilize parameterized reports in Shiny to allow for the user to input their own dataset (map). Thus, I specified a parameter and utilized params = ask in the render step. The main issue lies here:
Since the render step is under the for loop, it is basically run for each subject. As a result, the params ask interface loads up 50 times, asking for the user to provide their dataset each time.
Is there anyway I can avoid this? How can I get a user to supply their dataset file as a parameter, then utilize it for all 50 reports?

Answer 1

All your variables may be passed through in your render command, I do this for thousands of reports currently.
YAML of .Rmd template
This may include default values for certain parameters depending on your requirements, for illustrative purposes I have left them as empty strings here.
---
params:
var1: ""
var2: ""
var3: ""
---
Loading data set
In shiny, you can have the file input once and re-use for each report. Passing elements of the data frame to the render command in the next section.
Pseudo code for render in for loop
for (i in 1:n) {
rmarkdown::render(
"template.Rmd",
params = list(
var1 = df$var1[i],
var2 = df$var2[i],
var3 = df$var3[i]
),
output_file = out_file
)
}
Note: within a shiny app, you will need to use df()$var1 assuming the file input will become a reactive function.
You can then use the parameters throughout your template using the params$var1 convention.