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 (Maricopa County, AZ). 
  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 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