Sample Crude Rate Calculation and Regression Analysis

This example is an analysis of trends in colorectal cancer incidence rates from 1993-2013 in the SEER cancer registries. It will show you what information is needed to have Joinpoint compute Crude rates and how to provide that information to the Joinpoint program.

A crude rate is the number of new cases (or deaths) occurring in a specified population per year, usually expressed as the number of cases per 100,000 population at risk. When computing crude rates, Joinpoint allows you to display rates as cases per 1,000; 10,000; 100,000; or 1,000,000. Note that the population counts you place in the input data file should be the sum of the populations for all years included in the rate.

Using Joinpoint

There are four basic steps involved in generating any Joinpoint trend analysis. Review the description of the process, and then we will walk you through a regression analysis example using files created for this purpose.

  1. Creating an Input Data File for Joinpoint (or for this exercise you can use the files below created for this exercise)
  2. Setting Parameters in the Joinpoint Program
  3. Executing the Joinpoint Regression Program
  4. Viewing the Joinpoint Results

Creating an Input Data File for Joinpoint

The Joinpoint input file must be an ASCII text file. Refer to the Joinpoint help system for details concerning the format of this file. You may use SAS, SPSS, Excel, or any software package to create this text file.

The following input file is provided for this exercise:

When computing crude rates, Joinpoint requires the input data file to contain the necessary variables to compute the rates but also to have them in a specific order. Below is a list of the required variable order. Cohort-defining variables are only required when you have more than one cohort in your data file. All other variables in the list are required in order to have Joinpoint compute crude rates.

  • All cohort-defining variables (in this example it is “Sex”)
  • Independent variable (in this example it is “Year of diagnosis”)
  • Count
  • Population

Also, for the formulas used to compute crude rates and their associated standard errors, please reference the following help section: Dependent Variable.

Setting Parameters in the Joinpoint Program

The Joinpoint Regression Program requires that you specify parameters that are organized on three tabs: the Input File tab, the Method and Parameters tab, and the Advanced Analysis Tools tab.

Input File Tab

The Input File tab specifies the file format of the input data file and some additional settings for the model. Please refer to the Joinpoint program's online help for more information regarding the options on this tab.

Method and Parameters Tab

The Method and Parameters tab specifies the modeling method, constraints on the location(s) of the joinpoints, number of joinpoints, autocorrelated errors options, model selection method and AAPC confidence intervals. For this exercise, the default settings on the Method and Parameters tab tab were used.

Advanced Analysis Tools Tab

The Advanced Analysis Tools tab can be used to set up a parallel or coincident pairwise comparison or a Jump Model/Comparability Ratio Model analysis. The pairwise comparison is only relevant if you have one or more By Variables defined on the Input File tab. There will also be enhancements to this tab in the future that include multi-group clustering.

Executing the Joinpoint Regression Program

Once an input data file has been created and loaded into the session, and parameters have been selected, the program can be executed by clicking the lightning bolt on the Joinpoint toolbar or selecting Session>Execute on the menu bar. A progress meter will be shown on the screen while the Joinpoint calculation engine processes the data and generates the output. Note, it can take a few minutes to execute, depending on the size of the input data file and the options selected. After execution has completed, Joinpoint opens an output window to display the results.

Viewing the Joinpoint Results

For standard Joinpoint analyses, the output window displays the results on five tabs: Graph, Data, Model Estimates, Trends, and Model Selection. For Pairwise Comparison runs, an additional tab named Comparison will be shown. There is a cohort tree located to the left of the tabs which can be used to traverse the cohorts and various joinpoints in the analysis.

The results of your session are not automatically saved. If you close the output window without saving your results, you will need to re-run the analysis. The results can be saved to a Joinpoint output file (i.e. Sample.Crude.Rate.Calculation.Session.jpo) by selecting Save or Save As from the File menu, or by clicking on the disc icon on the toolbar. The results can be sent to a printer, PDF, Word, or Excel by selecting Print from the Output menu, and there are options to customize which elements of the output to include. The results can also be exported as text files and image files (for the graphs) by selecting Output>Export>Text… on the menu bar and making your selections. If you wish to export your results to an Excel spreadsheet, select Output>Export>Excel…

Running a Sample Crude Rate Calculation Analysis in Joinpoint

  1. Download the following file to use in this exercise by right clicking on the link and using Save Link As... to save the file on your computer:
    • Sample.Crude.Rate.Calculation.Data.txt is the data file containing the information needed to compute crude rates. You will use this file as the Input Data File for this exercise.

      The input data file for this example contains incidence counts and associated populations by sex and year of diagnosis.
  2. Open Joinpoint, and from the File menu, select New Session…. The Open file dialog will open.
  3. Browse to the folder where you saved the files for the exercise and open the Sample.Crude.Rate.Calculation.Data.txt file.
  4. The Joinpoint session window will open and will automatically have the Input File tab displayed. Below is a picture of the window you should see.

    Joinpoint session window

    The following options at the top of the screen should be automatically filled in:
    • File contains column headers - checked
    • Delimiters – Tab
    • Missing Characters - Space
    Joinpoint will display the first twenty records of the input file. Below the input file viewer are the controls that you need to fill in. Because you want Joinpoint to calculate crude rates, please set the following options:
    • Run Type: Calculated From Data File option
    • In the Type box please select Crude Rate
    • In the Rates Per combo box, please select 100,000
    Once you have made the previous selections, the screen should look like the following:

    Joinpoint session window

    Please make the following selections:
    • Count Variable – Select the “Count” variable from the list.
    • Population Variable – select the “Population” variable from the list.
    • Log Transformation – Yes {ln(y) = xb}
    • Independent Variable - select the “Year of Diagnosis” variable from the list.
    • Shift data points by - 0
    • Heteroscedastic Errors Option - Standard Error (Calculated)
    • By Variables – click the “Add…” button, select the “Sex” variable, and click Ok. You should see the “Sex” variable in the By Variables list.
  5. The last item that needs to be addressed on the Input File tab is to format the values of the Sex variable. The Sex variable has numeric values from 0 to 2 in the data file. Joinpoint provides the ability to display a text string in the output results for each numeric value of the By Variables. If you do not provide a format label for each value, then the numeric value will appear in the output. To have the output be more legible, we want to display labels (e.g. “Male and Female”, “Male”, and “Female”) instead of numbers. In order to build a format for the sex variable, first click on the Sex variable in By Variables box (once you do that the variable name will be highlighted). Then click on the “Define…” button located on the lower right-hand corner of the By Variables box. The “Edit Format” window will appear.

    Format labels must be entered as “value = label” in the format box at the bottom of the window. Please enter the following three “value=label” entries in the box.
    0=Male and Female
    1=Male
    2=Female
    The format screen should look like this when you are finished:

    Joinpoint session window

    Once you have entered the “value=Label” entries, click on the Ok button.

    The Input File Tab of your Session should now look like this:

    Joinpoint session window
  6. All the parameters on the Method and Parameters tab and Advanced Analysis Tools Tab will default to the correct settings. So, there is nothing to adjust on either tab.
  7. Click on the lightning icon on the toolbar to execute the session. The progress dialog opens showing the progress of the Joinpoint software. When it is complete, the Output Results dialog opens with the Graph tab displayed.
  8. To save the results so that they can be opened up later in Joinpoint without re-running the analysis, click on File>Save and choose an appropriate file name and location. Please note that when you save the results, you also save the session parameters with it. Once a results file is open, you can retrieve the session that was used to produce it by using the Output>Retrieve Session menu item. So, there is no need to save BOTH the session and output results to file.
  9. To export the results as files, click on Output>Export>Text… on the menu bar. The Export dialog will open. If you want to export the results as an Excel spreadsheet, click on Output>Export>Excel… on the menu bar. (As long as the Output Results window is on top, the Output menu is available. When the Session window is on top, it is replaced with the Session menu.)
  10. To save the session settings, click on the Session window so that it is active, then click on the disc icon on the toolbar or select File>Save on the menu bar. This will save the Joinpoint Session file (i.e. Sample.Crude.Rate.Calculation.Session.jps) with all the information you have loaded or set on each of the tabs above.

The following graph is the result of the session in the example for a maximum of 3 joinpoints. It is a scatter plot of the crude colorectal cancer incidence from SEER, for males and females from 1993 to 2013. A Joinpoint Model is also drawn on this graph. In this case, the model is four line segments joined at the joinpoints of 1995, 1998, and 2008. The model decreases until 1995, it increases again until 1998, decreases until 2008 and then decreases more until 2013. The APCs (Annual Percent Change) indicate the magnitude of the trend for each segment or time period.

This example is an analysis of trends in colorectal cancer crude incidence rates from 1993-2013 in the SEER cancer registries. The input data file used contains counts and populations which Joinpoint used to produce crude incidence rates and standard errors by year of diagnosis and sex. We used the SEER*Stat software to generate the counts (and associated populations) for colorectal cancer in the 9 SEER registries, 1993-2013.

Sample Joinpoint output window
Last Updated: 15 Apr, 2020