Tool 3: Determinants of Exposure

A Shiny application developed by the Industrial Hygiene team of the Department of Environmental and Occupational Health at the École de Santé Publique of the Université de Montréal (EPSUM) in collaboration with Ununoctium (Jean-Mathieu Potvin). Ununoctium designed the user interface (for versions greater than or equal to 4.0.0) and currently maintains the web application (but not scripts stored in scripts/).

Tool 3 uses the same patterns and mechanisms as Tool 1 (whenever possible) for consistency between applications of Expostats.

Introduction

This tool compares the underlying distributions corresponding to several categories of a variable of interest (e.g. presence / absence of ventilation, season of sampling, etc.). Data is entered as a spreadsheet file (Excel file) containing exposure levels and variables of interest. It exposes three main components.

1. Group risk assessment based on an exceedance fraction, a percentile, or the arithmetic mean.
2. Individual risk assessment based on an exceedance fraction, a percentile, or the arithmetic mean.
3. Comparison of two categories highlighting differences between their respective geometric means and geometric standard deviations, risk assessments, and probabilities that a prespecified difference exists.

Calculations are performed using a Bayesian model fit using a Monte Carlo Markov Chain (MCMC) engine. It assumes that the underlying exposure distribution is lognormal.

The underlying Bayesian models and data interpretation procedures are derived from best practices in industrial hygiene data interpretation techniques. They are thoroughly described in Expostats: A Bayesian Toolkit to Aid the Interpretation of Occupational Exposure Measurements (Annals of Work Exposures and Health, Volume 63, Issue 3, April 2019, Pages 267–279).

Requirements

TO BE COMPLETED.

R version 4.4.0 is required to work on and serve Tool 3 locally. These packages (and their transitive dependencies) are required.

• shiny
• bslib
• ggplot2
• ggimage
• htmltools
• rjags
• randtoolbox
• transltr

Usage

To serve Tool 3 locally, call

.run()

.run() is defined in .scripts/run.R.

Deploy

Tool 3 is deployed to shinyapps.io. To deploy a new version, call .pub().

# Deploy a beta version (useful for testing purposes).
# It is publicly accessible at https://lavoue.shinyapps.io/tool3-beta/.
.pub()

# Deploy an official (production) version.
# It is publicly accessible at https://lavoue.shinyapps.io/tool3/.
.pub("prod")

.pub() is defined in .scripts/publish.R.

Some environment variables are required to publish new releases with .pub(). They must be stored in a top-level .Renviron file as shown below. This file is ignored by Git and rsconnect.

# .Renviron
RSCONNECT_ACCOUNT_NAME=<account>
RSCONNECT_ACCOUNT_TOKEN=<token>
RSCONNECT_ACCOUNT_SECRET=<secret>

General Structure

The project is organized as a standard Shiny application as follows.

./
├── .local/
|   └── [temporary files ignored by Git scoped to each developer]
|
├── .scripts/
|   └── [scripts used while developing and ignored at runtime]
|
├── i18n/
|   └── [data used for internationalization (i18n) purposes]
|
├── man-roxygen/
|   └── [shared/common roxygen2 tags used more than once]
|
├── R/
|   └── [objects, constants, functions, etc.]
|
├── rsconnect/
|   └── [metadata on latest deployments]
|
├── scripts/
|   └── [official Expostats scripts and functions]
|
├── wwww/
│   ├── assets/
│   |   └── images/
|   |       └── [static images (any format)]
|   └── [static files served at runtime under root path]
|
└── [usual top-level source files]

Most objects are defined in .Rprofile, app.R, and in R/. For historical reasons, all Expostats functions are stored in scripts/. They are explicitly sourced at runtime by R/global.R. Other files are sourced automatically.

For more information on the structure, static assets, and naming conventions, read subsection General Structure of of Tool 1's README

Internationalization (i18n)

We are actively looking for external collaborators who could help us with supporting more languages. If you are interested, please send an e-mail to jerome.lavoue@umontreal.ca.

Tool 3 uses the same internationalization mechanisms and patterns as Tool 1. Please read subsection Internationalization of Tool 1's README for more information.

Styling

Tool 3 uses the same styling mechanisms and patterns as Tool 1. Please read subsection Styling of Tool 1's README for more information.

It is worthwhile to note that it is not necessary to include Bootstrap's assets (in the <head> of Tool 1) because bslib already does that automatically.

Known Issues

TO BE COMPLETED.

We may work on these issues in a near future.

• Inputs lack robust validation mechanisms and may lead to undefined behavior in some cases.

• Accessibility mechanisms (ARIA) are not implemented.

• Margins, aspect ratios, font sizes, font families, dimensions, and colors of all plots are inconsistent and must be standardized.

  • This could be achieved with shiny::getCurrentOutputInfo() and bslib::bs_current_theme().

• There are currently no explicit Terms of Service and Privacy Policy.

Bugs and Feedback

You may submit bugs, request features, and provide feedback by creating an issue on GitHub.

If you do not have a GitHub account, send an email to jerome.lavoue@umontreal.ca and jeanmathieupotvin@ununoctium.dev. Please use the following standard subject line:

Expostats [Tool 3] [Bug|Feedback]: <short description>