Syndrome Definition Evaluation 

name: syndrome_eval
fullname: Syndrome Definition Evaluation
description: >
  An automated report template that allows ESSENCE users 
  to evaluate the data details (line level) results of 
  one, two, or three syndrome definitions at a time. 
  Original Script By: Sara Chronister. 
  Revamped and Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. 
  National Syndromic Surveillance Program (NSSP). 
  Centers for Disease Control and Prevention (CDC).  
create_dir: true

Detailed Description

The Syndrome Definition Evaluation template (syndrome_eval) allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time. This template is adapted from Sara Chronister’s syndrome definition toolkit. Find her latest work here.

This template parses syndrome terms, identifies their type and count their CCDD matches.

The syndrome definition evaluation template generates:

  • A table summarizing individual definition information by syndrome definition
  • An interactive visualization comparing visits by syndrome definition over time
  • A comparative bar chart of total visits identified by all syndrome definitions combined
  • A summary table of the number and percent of identified visits captured by each observed combination of definitions
  • A Venn diagram, an Euler diagram, and an upset plot as visual representations of the number of identified visits captured by each observed combination of definitions
  • Summary plots of the top five occurring terms for each definition and each field of interest

User Inputs

  • NSSP Username: NSSP ESSENCE account username
  • NSSP Password: NSSP ESSENCE account password
  • Site: A participating site
  • Start Date: Automatically modified to be the first day of the MMWR week of the selected start date
  • End Date: Recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Automatically modified to be the last day of the MMWR week of the selected end date.
  • Has been Emergency: TRUE/FALSE option for limiting to emergency department visits
  • Chunk data pull (per day)?: TRUE/FALSE option for pull the data by chunks (time resolution: one day)
  • Grouping systems (Up to 3): When more than 3 are supplied, only the first 3 are considered by the template
  • Custom Query 1: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API
  • Custom Query Label 1: A string labeling Custom Query 1
  • Custom Query 2: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API
  • Custom Query Label 1: A string labeling Custom Query 2
  • Custom Query 3: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API
  • Custom Query Label 3: A string labeling Custom Query 3
  • A title for the report
  • Export Data: TRUE/FALSE option as to whether to save export and save datasets on the disk. When TRUE, a folder named Output is automatically created in the working directory and receives exported data in .csv format.

Output

When knit with parameters, this template generates a report in HTML format.

Add this template

# Add `syndrome_eval` to my existing Rnssp installation
Rnssp::add_rmd_template("syndrome_eval")

Remove this template

# Remove `syndrome_eval` from my existing Rnssp installation
Rnssp::remove_rmd_template("syndrome_eval")

Latest Update!

For questions, ideas for improvement/collaboration, or attribution, please submit an issue here.

Download this template