How to configure subdirectory service from Shiny Server

I have a Shiny server running, and I want to automatically build indexes at certain levels. My shiny-server.conf file looks like this:

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
  listen 3838;

  # Define a location at the base URL
  location / {

    # Host the directory of Shiny Apps stored in this directory
    site_dir /www1/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;

    ## RGA want to run as apache not root
    run_as shiny;

    log_file_mode 0644;

    #preserve_logs true;

       ## Define a location at the IntroStats directory
       location /IntroStats {

          ## When a user visits the base URL rather than a particular application
,
          ## an index of the applications available in this directory will be sho
wn.
	  directory_index on;
        } 
	  	
  }		
}

Rmd files placed in the top level directory work as epected:
https://pluto.coe.fsu.edu/rdemos/NormalCalculator.Rmd

But Rmd files placed in the IntroStats directory fail because they various js files won't load.
https://pluto.coe.fsu.edu/rdemos/IntroStats/EffectSize.Rmd

How should I be setting my configuration to fix this?