An official website of the United States government
Surveillance Research Program

Example 4

An example of male brain cancer for phase of care estimation.

Objective

Calculate U.S. Male brain cancer phase of care estimates.

 

Steps

  1. Before we get started, please download and save the following .dic and .txt files to your computer. These files will be needed in a later step.

  2. If the user wishes to see the SEER*stat files used to create these data files, then can be found here.

  3. Start the ComPrev application.

  4. Select File, New Session from the menu.

  5. For Type of Session, select Phase of Care. Then press the Next button at the bottom of the window.

  6. Since you are using the built in data file for ComPrev, just press the Next button on the Inc\Surv Parameters tab.

  7. On the POC LDP tab, you will need to select your LDP data dictionaries. Under step 1, where it says DIC File, press the Browse button. In the Open File dialog that is displayed, navigate to where you downloaded the file US.39year.brainandcns.2014.male.by.singleage.dic, and select the file, and press the Open button. You may get a warning that the corresponding data file was not found in the folder, but that's okay, it found the data file in the same directory. Just press OK on the warning dialog.

  8. Now proceed and select a DIC file under step 2 using the file US.40year.brainandcns.2015.male.by.singleage.dic. You may get a warning, but just hit OK.

  9. Next press the Mapping... button under Step 3 "Map To Existing Data". The Data Mapping window will be displayed. This window lets you tell ComPrev how to map your data file to its internal data. At the top of the window, you will see 3 combo boxes. For the ComPrev Field "Site", press the combo box arrow button under the LDP Field and select "Brain and Other Nervous System". For the field "Race", you do not need to do anything since Comprev has defaulted the selection to the variable "Race recode". Finally, for the field "Sex" select "Male". Press the OK button.

  10. Back on the Session Setup window - POC LDP tab, press the Next button. On the POC Survival window, you will see a radio button for SEER*Stat Survival (Crude Probability of Death) Import File. Please select it. Click the Browse button on the line that says "DIC File:" and select the brain.and.cns.survival.for.POC.males.dic file from above. You will get a Warning message which states "Lack of data detected for some durations in the Survival Matrix". This is Comprev indicating that some of the values in the data file were blank and it filled them in for you. This is common in Survival files exported from SEER*Stat. Press the OK button. Press the Next button.

  11. On the Selections tab, click Next.

  12. On the Settings tab, you can see that most of the information is already filled in for you. The Prevalence Date is 2014, the Initial Data of Diagnosis is 1975, and the Age Groups is set to "Single Ages". Press the Finish button at the bottom of the window.

  13. A Progress Window will be briefly displayed while ComPrev is calculating the Phase of Care statistics. When they are done, the Main window will be displayed.

  14. On the left side of the Main Window, the list of cohorts to view are displayed. Since we only had data for one cohort, we just have the Brain and Other Nervous System \ All Races \ Male cohort available.

  15. On the right side of the Main Window, 5 tabs are displayed.

    • Incidence: You can view the incidence parameters used by ComPrev as a table or graph.

    • Survival: You can view the survival parameters used by ComPrev as a table or graph.

    • Completeness Index: Contains a table with completeness index and standard error (if requested) by age at prevalence as well as a graph of the completeness index.

    • Phase of Care: Displays Phase of Care information, which also contains LDP and Complete Prevalence.

    • Settings: Displays all of the information you specified to create this session.

  16. The Phase of Care tab is the only new tab. See the help for information on the Incidence, Survival, Completeness Index, and Settings tabs. On the Phase of Care tab, there are several columns. Each column has a sub-column and attention should be paid. For instance, the Phases of Cancer are listed for Limited Duration in columns 4 - 8, and for Complete Prevalence in columns 9 - 13.

    • Age : the age, or age group for that line. This is age at the prevalence date determined by the FIRST LDP file.

    • Completeness Index, Percent : The Completeness Index for the age listed in "Age".

    • Completeness Index, SE : The standard error of the Completeness Index.

    • Initial phase (under "Limited Duration Phase of Care"): The observed incident cases of age x who were diagnosed between Jan 1 and Dec 31 in the year before prevalence date.

    • Continuing phase (under "Limited Duration Phase of Care"): The observed incident cases of age x who are neither in the initial phase, nor the final phase.

    • EOL Cancer (under "Limited Duration Phase of Care"): The observed cases of age x who died of the the specific cancer during year Y (and therefore are in the final phase on 1/1/Y).

    • EOL Total (under "Limited Duration Phase of Care"): The observed total number of cases of age x who died of the specific cancer OR other causes during year Y. Using the number of (EOL Total - EOL Cancer), one can determine the number of cases who died of other causes in year Y.

    • Total (under "Limited Duration Phase of Care"): The observed total number of incident cases across all phases, initial, continuing, and EOL Total.

    • Initial phase (under "Complete Prevalence Phase of Care"): The observed incident cases of age x who were diagnosed between Jan 1 and Dec 31 in the year before prevalence date. There are no unobserved initial phase cases, so this number matches LDP.

    • Continuing phase (under "Complete Prevalence Phase of Care"): The observed plus unobserved incident cases of age x who are neither in the initial phase, nor the final phase.

    • EOL Cancer (under "Complete Prevalence Phase of Care"): The observed plus unobserved cases of age x who died of the the specific cancer during year Y (and therefore are in the final phase on 1/1/Y).

    • EOL Total (under "Complete Prevalence Phase of Care"): The observed plus unobserved total number of cases of age x who died of the specific cancer OR other causes during year Y. Using the number of (EOL Total - EOL Cancer), one can determine the number of cases who died of other causes in year Y.

    • Total (under "Complete Prevalence Phase of Care"): The observed plus unobserved total number of incident cases across all phases, initial, continuing, and EOL Total. This number is also complete prevalence for each age.

    • Population : Population for each age for year Y.