AutomatedExceedanceDescriptiveEpi

An automated system to produce descriptive epidemiology for Public Health England SGSS exceedance reports

Production of the report is a two-stage process, described below.

Stage 1: Obtain a linelist from SGSS

• This is an SQL query (produced by our local information team) where the user can specify a number of parameters to retrieve the appropriate data (important filters include the organism of interest, the centre and the start/end specimen dates – further data filtering can be performed in Stage 2)

• Deduplication is embedded within the query

• The SQL query is titled SGSS_Extract_Data_Descriptive_Epidemiological_Report_SEaL.sql

• The user guide is titled User Guide.docx

• For more information contact Jordan Wilson (jordan.wilson@phe.gov.uk)

Stage 2: Generate the automated exceedance descriptive epi report using R

• A Microsoft Word report is generating using a series of R scripts and a single Rmd script

• The user may specify a number of parameters depending on the desired output (these include filters to specify appropriate reporting dates, age, sex, local authority, laboratory, requesting organisation, specimen type and travel, as well as figure aesthetics)