Preparing Data for Analysis National Center for Immunization & Respiratory Diseases Influenza Division Nishan Ahmed Regional Training Workshop on Influenza Data Management Phnom Penh, Cambodia July 27 – August 2, 2013

Check for accuracy of observations and correct or eliminate inaccuracies – Important for both simple and complex data Questions to ask: – Are values outside of what you would normally observe? – If yes, are values due to inaccuracies in the data or to real changes in activity (i.e. an outbreak, start of influenza season) Values can be inaccurate due to many factors Data Entry mistake Incorrect measurement at site Incorrect analysis Data Cleaning: What is it?

To prepare your data for regular analysis – Steps: Prepare a copy for temporary cleaning, but also clean the original data source as corrections are validated If data is not cleaned at source, cleaning will need to be done each time analysis is attempted (i.e. records can be temporarily deleted until verified or corrected) To finalize a dataset for future analysis/create a clean copy to be used for research – Typically a more thorough process than cleaning during a flu season Data Cleaning: Why do it?

To check for validity and consistency of reported variables – Ensures that the data collected makes sense Examples: – # of ILI cases is not greater than the # of patient visits – The date of onset is before data of death – Only enrolled sites should be reporting & included in analysis of sentinel data To check for data outliers – A facility that normally sees ~100 patient visits will probably not see 1,000 patients during a week To identify and remove duplicate records Data Cleaning: Why do it?

How do you find data that has problems? – Eyeball method – Through quick, simple data queries Access or Excel queries as you go – Statistical methods – Through pre-programmed automated processes Used for elements that are routinely cleaned Example: Automated process for deleting duplicate records Methods to identify problems

Eyeball Method

To find duplicate records, using Access Quick and Simple Queries

To check validity of variables Quick and Simple Queries

Automated Processes: Duplicates

Measures of Center – Mean: Sum of the observations divided by the number of observations. – Median: The middle value in an ordered list – Mode: The most frequently occurring value Basic Statistic Measures Measures of Variation or Spread Standard Deviation: measures variation by indication how far, on average, the observations are from the mean

Equations in Excel MeanMedian Standard Deviation

Example: Checking for outliers – The US ILI system uses a statistical process to check for outliers: Look at # of patient visits over time from a given provider That # should be consistent within a certain degree of change (i.e. 4 standard deviations from the mean) All values above or below this value are selected and checked manually to verify whether or not the values are reasonable and make sense. Data Cleaning Processes

Data Outliers in Excel

Data Cleaning 01002: Data could not be disproved, left in : Fixed data based on returned workfolder 04108: Data looked OK to surveillance staff, this was the peak of pandemic, and we would have expected numbers to be high

List of errors found during the cleaning process Helps to keep track of changes made to records during the cleaning process. – Keep track of how the data has changed over time – Used for follow-up on questions to sites May be manual or automated – Based on needs of the data Error Logs

Example of Error Log DateState Specimen ID Patient IDFieldPrior Value Current ValueReason for Change Your InitialsComments 2/9/11MDA SPECIMEN idA A b coinfection H3 and 2009 H1N1AB changed one specimen id to 'b' so would be coded as two separate viruses 2/9/11MDA SPECIMEN idA A b coinfection H3 and 2009 H1N1AB changed one specimen id to 'b' so would be coded as two separate viruses 2/9/11MDA SPECIMEN idA A B coinfection B and 2009 H1N1AB changed one specimen id to 'b' so would be coded as two separate viruses 2/9/11SD M11VR SPECIMEN id M11VR M11VR (a, b, c) coinfection 2009 H1N1, H3, and BAB changed one specimen id to 'b' so would be coded as two separate viruses

Preparing data for analysis includes finding and cleaning as many data errors as possible – Statistical methods, the eyeball method, and simple queries can all be used to find potential data errors Data cleaning is important because data errors could alter the interpretation of data (i.e. could cause a perceived increase without a true increase in disease activity) Error logs are useful in accounting for errors and how they were dealt with Conclusions