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File Preferences
Access the File Options by selecting Options from the File menu. Make changes to the fields as necessary. When you are finished, click SAVE and then CLOSE.
Default Data Directory
The default directory to be used when browsing for your data from a Joinpoint session can be set here. In order to set the directory, use the browse button and select the directory to be used as the default.
Display Splashscreen on startup
When the Joinpoint program is started, a splashscreen will automatically appear for 5 seconds. This option can be used to display or hide the screen.
Maximum Number of Threads
With the introduction of processing multiple cohorts simultaneously (threading), an option to adjust the number of threads is provided. The number of threads that Joinpoint will try to use when running a session can be set here. There number cannot be set above the maximum for the computer that Joinpoint is installed on.
A reason to lower the number of threads is to provide other concurrently running Windows programs more resources under Windows. The more threads that Joinpoint tries to use, the slower other concurrently running Windows programs might run.
Turn on all Joinpoint warning messages
Joinpoint has various 'nag' warning messages that appear to users to warn them of potential problems. A 'nag' warning is a warning that users can choose to turn off and when turned off it will remain off until this option is adjusted. When this button is clicked, all 'nag' warning messages previously turned off will be turned back on.
Session Preferences
Access the Session Preferences window by selecting Options ( 
) from the Session task bar (only available when a session is open). Make changes to the fields as necessary. When you are finished, click OK.
Alpha Levels
Joinpoint Locations - The significance level used to test the Type I error when selecting a model. The default value for this field is 0.05. Alpha level values must be greater than 0 and less than 1.
APCs - The significance level used to test whether an APC value is significantly different from zero. The default value for this field is 0.05. Alpha level values must be greater than 0 and less than 1.
AAPCs - The significance level used to test whether an AAPC value is significantly different from zero. The default value for this field is 0.05. Alpha level values must be greater than 0 and less than 1.
Jump Value and Comparability Ratio - The significance level used to test whether a Jump Value or Comparability Ratio is significantly different from zero. The default value for this field is 0.05. Alpha level values must be greater than 0 and less than 1.
Permutation Test Seed
Typically, you should allow the computer to use the default seeds for the random number generator. By using these default seeds, one can duplicate results from a previous Joinpoint session even though the program uses Monte Carlo sampling. Although not recommended in general, the Joinpoint Regression Program allows one to change a default seed here. The default value is 7160.
Empirical Quantile Seed
For the Empirical Quantile confidence interval calculation method, you can adjust the value of the seed used for the random number generator involved with producing the resampled residuals for each cohort. To set the initial seed value, use the "Seed Value" text box. The default value is 10,000.
The seed can be kept constant or changed for each cohort. The seed options are:
Constant Seed - this option will keep the seed the same for all cohorts in your data file. The seed used will always be the number in the "Seed Value" text box.
Varying Seed - this option will change the seed for each cohort in your data file. The first cohort in your data file will use the seed value set in the "Seed Value" text box. For each cohort after that, the seed is computed using the following formula: (Initial Seed Value * Cohort Number) + (Cohort Number - 1). The "Initial Seed Value" is the value set in the "Seed Value" text box. The "Cohort Number" is the number of the cohort that is being processed. The first cohort in the data file is 1, the second 2, etc.