Slide 1

Overview of Link Plus

Probabilistic Record Linkage Software

logo NPCR National Program of Cancer Registries

Logo Registry Plus

Logo Department of Health and Human Services

Logo of Centers for Disease Control and Prevention

Slide 2

Acknowledgements

Slides adapted from training materials developed by CDC-NPCR Faculty:
Melissa Jim, CDC/IHS melissa.jim@ihs.gov
David Espey, CDC/IHS david.espey@ihs.gov

CDC/Link Plus development and training:
Kathleen Thoburn
David Gu

Adapted by:
Megan Hoopes, NW Tribal Epidemiology Center ideanw@npaihb.org

logo NPCR National Program of Cancer Registries

Logo of Centers for Disease Control and Prevention

Logo Department of Health and Human Services

Slide 3

• Stand-alone probabilistic record linkage program
• Combines ease of use and statistical sophistication
• Detects duplicates within a single database, or links 2 database files
• Supports North American Association of Central Cancer Registries files, fixed width files, delimited files, and CRS Plus database

Slide 4

Link Plus Software

• Can handle missing values of matching variables
  • automatically treats null or empty values as missing data and allows user to indicate additional values to be treated as missing data
• Facilitates blocking ("OR blocking") by indexing the variables and comparing the pairs with the identical values on at least one of those variables
• Provides support for manual review of uncertain matches

Slide 5

Link Plus Is Free

$0.00

Slide 6

Link Plus Is Easy To Use

Link Plus gets you from HERE:

Cancer Registry data for John Smith:

Last name	First Name	Site	SSN	DOB	Sex	DateDx
SMITH	JOHN	C619	123654789	02111934	1	06152004

Vital Statistics data for John Smith:

Last name	First Name	DOB	Date of Death	COD	Death Cert #
SMITH	JOHN	02011934	03202006	123654789	01234

Slide 7

Link Plus Is Easy To Use

To HERE:

Linked data for John Smith:

Last name	First Name	Site	SSN	DOB	Sex	DateDx	Date of Death	COD	Death Cert #
SMITH	JOHN	C619	123654789	02011934	1	06152004	03202006	C100	01234

Slide 8

Link Plus Is Easy To Use

Without having to go HERE:

Two complex statistical equations used as examples of what is NOT required due to the fact that Link Plus is easy to use and the mathematics are largely hidden from the user.

Slide 9

Link Plus Is Easy To Use

• Designed especially for cancer registry work
  • HOWEVER, can be used with any data
• Mathematics largely hidden from user
• Practical default values supplied for many tasks
• Familiar Windows interface
• Includes Help and test examples

Slide 10

Using Link Plus

Slide 11

Obtaining/Updating Link Plus

logo NPCR National Program of Cancer Registries

Logo Registry Plus

1. Go to NPCR Home Page http://www.cdc.gov/cancer/npcr
2. In the 'Software and Tools' Section
   - click on Registry Plus
3. Under 'Registry Plus Components'
   - click on Link Plus - Download

Slide 12

Getting Started

• Make sure you know your data!
• Review and clean data files
• Frequency distributions very helpful
• Look for errant values
  - e.g. - DOB day component = 16

Slide 13

Data Cleaning Tips

• Last Name
  - Link Plus automatically cleans punctuation and strips off suffices, numbers III
• First Name
  - May find Dr. Bill or Rev Bill or Sister Mary
  - Remove prefix in First Name field
• Middle Name
  - Link Plus automatically cleans numbers, weird symbols
  - Link Plus accounts for the switching of first and middle names
  - NMI-no middle initial or NMN-no middle name
• DOB
  - Review day, mo, yyyy component
  - Replace errant values with missing
• Sex
  - Make sure files use same coding convention; M, F, or Blank OR 1, 2, 9

Slide 14

Linkage Overview

Two main types of linkage:

• Linkage of 2 files
  - Probabilistically link one file to another file
• Deduplication
  - Special case of record linkage
  - Records in the same file are blocked, compared, and scored against each other
  - Result is a ranked list of record pairs
  - High-scoring pairs may be duplicates

Slide 15

Linkage configuration screen

Image of Link Plus Linkage Configuration screen.

Slide 16

File Import File 1 versus File 2

• File 1 and File 2 have a one to many relationship
  - File 1 (ONE); File 2 (MANY)
• Death record is File 1; cancer registry is File 2:
  - One John Smith in death record file can link to many John Smith's in cancer registry file
• Cancer registry is File 1; death record is File 2
  - One John Smith in cancer registry file can link to many John Smith's in death record file

Image of Data Type area of Link Plus Linkage Configuration screen showing Data Type and File 1 and File 2 fields.

Slide 17

File Layout

• After designating File 1 and File 2, specify file layout for each file
• Link Plus reads .txt files:
  - Fixed width
  - Comma delimited
  - Tab delimited
• Link Plus provides view of first 20 records of each input file
  - Verify that data is being read in properly

Slide 18

Blocking Variables

• Exact matches
• Blocks of data to compare variables within
• Common blocking variables are:
  - Last Name
  - First Name
  - Social Security Number
  - Date of Birth

Image of Select Blocking Variables area of Link Plus Linkage Configuration screen showing Data Item (File 1), Data Item (File 2), and Phonetic System fields.

Slide 19

Phonetic Systems

• Phonetic coding involves coding a string based on how it is pronounced
• Link Plus offers a choice of 2 Phonetic Coding Systems:

Soundex

• Code for a name consisting of a letter followed by three numbers: the letter is the first letter of the name, and the numbers encode the remaining consonants
• Reduces matching problems due to different spellings
• Simple and fast

Slide 20

Phonetic Systems

New York State Identification and Intelligence System (NYSIIS)

• Maps similar phonemes to the same letter; maintains relative vowel positioning
• String can be pronounced by the reader without decoding
• Improvement to the Soundex algorithm
  - More distinctive; people are more likely to have the same Soundex than the same NYSIIS
  - Reported accuracy increase of 2.7% over Soundex
  - Studies suggest NYSIIS performs better than Soundex when Spanish names are used
  
• However, Soundex may bring more pairs for comparison when it used for blocking

Slide 21

Matching Variables

• Up to 10 fields may be selected for matching
• Recommended variables (Matching Methods):
  - Name--Last (LastName)
  - Name--First (FirstName)
  - Name--Middle (MiddleName)
  - Sex (Exact)
  - Race (Exact)
  - Birth Date (Date)
  - Social Security Number (SSN)

Image of Select Matching Variables and Methods area of Link Plus Linkage Configuration screen showing Data Item (File 1), Data Item (File 2), and Matching Method fields.

Slide 22

Matching Methods

• Exact
  - Case insensitive character-for-character string comparison method
  - Results are either yes or no
• Generic String
  - Uses edit distance function (Levenshtein distance) to compute the similarity of two long strings
  
  • Minimum number of operations (insertion, deletion, or substitution of a single character) needed to transform one string into the other
• Last Name/First Name
  - Incorporate both partial matching and value-specific matching to account for minor typographical errors, misspellings, and hyphenated names

Slide 23

Matching Methods

• SSN
  - Specifically for Social Security Number
  - Incorporates partial matching to account for typographical errors and transposition of digits
• Date
  - Incorporates partial matching to account for missing month values and/or day values
• Middle Name
  - Accounts for occurrence of the middle initial only versus the full middle name

Slide 24

Matching Methods

• Value-Specific (Frequency-Based)
  - Intended for advanced users
  - Sets weights for matching values based on the frequencies of values in the two files being compared
  - A match on a frequent value is associated with a low weight, while a match on a rare value is associated with a high weight
  - In a file with a high proportion of records with a white race (value of 01), a match on value 01 would be weighted lower than a match on the value 03 (American Indian

Slide 25

Missing Values

• Automatically treats null or empty values as missing data for Matching Variables
• Allows user to indicate additional values which are to be treated as missing data by the program
• Specify date format on the missing value grid when the Date Matching method is applied to a matching variable

Slide 26

Missing Values

• Specify date format on the missing value grid

Image of setting the date in the Missing Value (File 2) field of the Link Plus Configuration screen.

Slide 27

Direct Method

• "Direct Method" refers to the method used to derive the M-Probabilities used in linkage
  - Probability that a matching variable agrees given that a comparison pair is a match
• Click if you prefer to use the default M-Probabilities or user-defined M-Probabilities
• Click on Advanced to view the default M-Probabilities or define your own
• Un-click if you prefer Link Plus to compute the M-Probabilities based on your data using the EM algorithm

Slide 28

EM Algorithm

• Expectation-Maximization algorithm
• Method for maximum likelihood estimation in problems involving incomplete data
• Unclick Direct Method if you would like Link Plus to compute the M-Probabilities based on your data
  - Estimates reflect the characteristics of the data dynamically
• Very popular computational method
• Basic principle is to derive a solution in a complicated case from a corresponding solution in a simple case

Slide 29

Cut Off Value

• The score value above which comparison pairs are accepted as potential links and presented for review
• Value should always be positive
• Initial value of around 7 recommended when using the recommended Matching Variables
• Run linkage, and quickly review potential matches to identify upper and lower cut off scores
  - Upper cut off = where do "perfect" matches end?
  - Lower cut off = where do non-matches begin?
  Example:
  - Solid matches somewhere between 20-30
  - Non-matches 10-20
  - Solid = 27 and higher, and Non-matches = 17 and lower
  - Gray Area = Greater than 17 and less than 27

Slide 30

Manual Review of Uncertain Matches

Graphic of Link Plus Linkage Report screen showing uncertain matches highlighted for manual review.

Slide 31

Manual Review of Uncertain Matches

• Once Cut Off scores have been identified

Graphic of Link Plus Assign Match Status dialog showing the Select all as true matches radio button selected.

Slide 32

Manual Review of Uncertain Matches

• Manual review screen provides special sorting that always keeps the comparison pairs together
• Fields that are not on the linkage report can be included for manual review
• Users can switch between the two viewing modes: the Datasheet View and the Pair view
• Match status may be assigned manually, or may be assigned automatically by match score

Slide 33

Manual Review of Uncertain Matches

• Includes the option to restrict view to only uncertain matches
• Individual columns may be sorted, hidden and unhidden from view, and re-sized
• Order of the columns on the review screen may be modified
• Review sessions may be saved and re-opened at a later time
• Allows two reviews to be compared so that the difference can be resolved into a final review file

Slide 34

Tips for Manual Review

• Focus initially on SSN and DOB
  - Names have a lot of issues (spelling and spacing)
• Once matches on SSN go away, pay attention to DOB, name, and sex
  - First and middle name switches are common
• Use race & address variables if available
• First time you start doubting if a pair is a match
  - Score will be upper cut off score
  - Anything above is considered a match
• When start to see junk - Score will be lower cut off score
  - Anything above is considered a match
• Keep an eye out for - Husbands and wives matching (SSN's match/sex different)
  - Brothers, sisters, and twins (LN match, SSN off by 1)
• Two people should review so that results can be combined and resolved
• These are suggestions - need to know your own data

Slide 35

Helpful Link Plus Tips

• With real data Link Plus may take awhile to read data files
• Be patient - Linkage times vary
  - IHS Linkage (2.4 million records)
  With VS Data:
  
  • Oregon: 2 hrs/400,000 recs
  • Michigan: 6.5 hrs/1,207,000 recs
  With Cancer Registry Data:
  
  • Oregon: 36 min/94,172 recs
  • California: 13 hrs/1,935,255 recs
• Wait (but not days) - something went wrong
  - Can run out of virtual memory
• Takes a lot of CPU
  - Shutdown and restart computer right before linkage to clear up as much space as possible prior to linkage
  - Turn off screen saver/Close all other programs