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Immunization Charts

Introduction

This project provides an approach to the creation of custom immunization history charts. These charts can be generated as part of notice letters for overdue Immunization of School Pupils Act (ISPA)-mandated or Child Care and Early Years Act (CCEYA)-mandated immunizations.

Usage

Environment

R is used with LaTeX (via rmarkdown) for PDF generation. renv is used in this repository to assist with accurately reproducing the R project environment.

Data

This project is intended to be used with data extracts from Panorama PEAR.

Input files, in xlsx format should be organized in a subfolder input (out of caution, input and output folders are .gitignored, and need to be recreated by the user). Each xlsx file should have a shared format. It's suggested that xlsx exports from Panorama PEAR are batched by client birth year. The report must at minimum include "Client ID", "Date of Birth", and a string representation of the immunization history, in a column "Received Agents". To create this immunization history string, a "Repeater" Data Container must be used in the Panorama PEAR report builder. The repeater will be formatted as:

  1. [PresentationView].[Immunization Received].[Date Administered]
  2. Text box with space, dash, and a space (-)
  3. [PresentationView].[Immunization Received].[Immunizing Agent]

Functionality

make_charts.R contains data processing steps, with some functions relating specifically to formatting information for use in LaTeX code separated out into latex_utilities.R. Based on your particular report, adjust the col_types and selected columns for your particular data file(s) in make_charts.R.

chart_template.Rmd allows for generation of PDF files using LaTeX, by inserting processed data elements into LaTeX code. This LaTeX code can be customized and expanded upon such that the immunization chart is an element in a larger letter with:

  • Addressee information that can be shown in the window of an envelope
  • Public Health Unit branding
  • List of overdue diseases
  • Public Health Unit-specific instructions for updating vaccination records or consultation on vaccination
  • Any other customizations that can enhance client experience or streamline vaccine record management operations

This project currently supports charts that include any combination of CCEYA and ISPA-mandated vaccinations, in addition to HPV and Hepatitis B recommended vaccines.

These diseases can be re-ordered to suit your application, through modifications in the parameters section in make_charts.R. Any diseases left off generated charts will be collapsed into the 'Other' diseases column.

vaccine_reference.xlsx includes the specific vaccine values currently supported, and the diseases they immunize against for the purposes of indicator dots on the immunization history chart output. Create an issue or pull request to add more vaccines.

An output subfolder should also be created for generated PDFs, and a leger of vaccines detected in the Received Agents in your data file(s).

Note that immunization history for a single client can exceed a single page. For large mailing campaigns utilizing a envelope stuffing machine, you will need to separate these clients out from those with records that fit on a single page.

Testing

test.R generates a data file with vaccination history for a single client, which can be used with make_charts.R with default parameters. This client receives every vaccine in vaccine_reference.xlsx (one per week). Running test.R will create input and output subdirectories, create the test data, and generate a PDF notice for the client.

Contributing

Fixes or additions to the vaccine_reference.xlsx, dependency updates, documentation improvements, and additions of tests will enhance the usability and reliability of this project and are welcome contributions.