SEER*Stat Rate Exercise 6: Mortality Rates by County Attributes

County attribute data from the US Census such as median income or educational attainment are linked to SEER incidence, US mortality, and population data by state-county FIPS codes.

Create a table showing mortality rates for the US population by high school education quintiles. Assign quintiles of counties so that 20% of the counties are in each group. Start with the results from Rate Exercise 5 to use the quintile variable created in that session. Results should be based on data for female malignant cervical cancer cases for the years 2006-2010.

Key Points and Reminders

  • US mortality databases are only available when using SEER*Stat in client-server mode.
  • This exercise illustrates the use of SEER*Stat to view mortality rates by county attribute variables.
  • Using results from Rate Exercise 5, see how to retrieve a user-defined variable from a saved matrix for use in a new session.
  • When a new database is selected in an existing session, the base variables may differ between databases. If a variable used in the original session is not available in the new database, the Invalid Session Variable Definitions dialog will open to allow you to make corrections.

Step 1:  Open Exercise 5's Matrix

  • Start SEER*Stat.
  • From the File menu select Open > Rate File or use the Any SEER*Stat File button on the toolbar.
  • Open the file saved in rate exercise 5. The filename should be "Rate Exercise 5.sim".
  • If you did not save the output for exercise 5 you may open our version of the output: Exercise 5 Matrix Results.

Step 2:  Extract the Session

  • SEER*Stat matrix files include the session information used to generate the table. This information serves as documentation for the results and provides a convenient method for generating similar statistics.
  • From the Matrix menu select Retrieve Session.
  • Two windows should now be open. Close the matrix window containing the results calculated in exercise 5. You should now have one window labeled "Rate Session-x" where x is the number of rate session windows that you have created since starting SEER*Stat.

Step 3:  Select a Database (Data Tab)

  • In Rate Exercise 5, we created a table showing SEER incidence rates. In this exercise we want to show US mortality rates, which requires a database change.
  • On the Data Tab select "Mortality - All COD, Aggregated With County, Total US (1969-2010) <Katrina/Rita Population Adjustment>".
  • The Invalid Session Variable Dialog will open because the year of diagnosis used in the Pop/Case Selection and site recode variable used in the Case Selection are not in the mortality database.

Learn More...

Certain databases are only available to SEER*Stat users who access data in client-server mode. US mortality data are not distributed on the SEER*Stat DVD and in the downloadable compressed data files. For more information about data access options, see the SEER Research Data Web site.

Step 4:  Edit the Invalid Variables

To edit the year of diagnosis variable:

  • Open the Pop/Case Selection editor by selecting "Year of Diagnosis" and clicking Edit.
  • In the Selection Statement section, select the following line to edit:
    {Race, Sex, Year Dx, Registry, County.Year of diagnosis} = '2006','2007','2008','2009','2010'
  • Replace the year of diagnosis selection statement with the following for year of death:
    {Race, Sex, Year Dth, State, Cnty, Reg.Year of death recode} = '2006-2010'
  • Click OK to save your changes. The variable's status on Invalid Session Variable Dialog dialog will change to "Ok/Resolved"

To edit the site recode variable:

  • Open the Case Selection editor by selecting "Site recode ICD-O-3/WHO" and clicking Edit.
  • In the Selection Statement section, select the following line to edit:
    { {Site and Morphology.Site recode ICD-O-3/WHO 2008} = 'Cervix Uteri'
  • Replace the site recode selection statement with the following for cause of death:
    {Site and Morphology.Cause of death recode} = ' Cervix Uteri'
  • Click OK to save your changes. The variable's status on Invalid Session Variable Dialog dialog will change to "Ok/Resolved"

Step 5:  Open the Dictionary Editor

  • Open the SEER*Stat dictionary editor by selecting Dictionary from the File menu, or using the Dictionary button on the toolbar.
  • Use the "+" to expand the "User-Defined" category.
  • You will notice that the "Quintiles - % < hs education 2000" variable created for exercise 5 is available for use in this session with the mortality database.
  • To have this variable available in future sessions that use the same database:
    • Double-click on the variable name, Quintiles - % < hs education 2000", to open the Edit Variable window.
    • Check the Save to Dictionary option.
    • Click OK to close the window.
  • Click Close to exit the data dictionary.

Learn More...

  • A unique dictionary is associated with each SEER*Stat database. The dictionary consists of variables which describe the data fields in the database. Both the incidence database and mortality database used in exercises 5 and 6 are linked to county attribute data from the US census, so the quintile variable is available in both sessions.
  • Variables that are not saved to the dictionary will only be available in the current session (including when that session is re-opened or retrieved from a matrix). Variables that are saved to the dictionary will be available in future sessions which use the same database.

Step 6:  View the Session Tabs

Since we extracted this session from exercise 5's matrix file, most of the tabs have the correct settings. Take a look at each tab.

  • We already changed the Data Tab to use the mortality database.
  • There are no changes to be made on the Statistics Tab -- age-adjusted rates and the correct parameters should already be selected.
  • Move to the Selection Tab. The "Race, Sex, Year Dx, Registry, County (Pop, Case Files)" and "Other (Case Files)" selections were updated when the invalid variables were edited in Step 3. No further changes are needed.

Step 7:   Verify the Table Tab

  • Move to the Table Tab.
  • "Quintiles - % < hs education 2000" is listed as the row variable. This user-defined variable created in Rate Exercise 5 contains the high school education quintiles needed for this exercise. No changes are needed.

Step 8:  Review the Title

  • Move to the Output Tab.
  • Remember that you are working with a session that was extracted from exercise 5's matrix file. Therefore, change the title to reflect we are displaying mortality rates for the US and that this is exercise 6:
  • Age-Adjusted Mortality Rates for Female Cervical Cancer, Total US, 2006-2010
    By Quintiles (Based on Total US Counties) of Percentage of Population (Ages 25+) without a High School Degree or Equivalent
    Rate Exercise 6

Step 9:  Execute SEER*Stat and Save the Matrix

  • At this point, you have made all the necessary selections on the session tabs. Use the Execute button or select Execute from the Session menu to execute the session.
  • A new window will be opened containing the output table or matrix. Results shown in the SEER*Stat matrix window cannot be edited. You can print the matrix, export the results to a text file, and copy-and-paste data into other applications. The Results Matrix section of the help system contains more information about the SEER*Stat matrix and its features.
  • Use the Save As command on the File menu to save the matrix. Enter "Rate Exercise 6" as the filename. SEER*Stat will assign the "sim" extension to indicate that this is a "SEER*Stat Rate Matrix" file.
  • Compare your results to this SEER*Stat matrix file: Rate Exercise 6 Matrix Results.