The Run Window appears when you click on the Run menu option. This window allows you to specify the Run Title, Model Name, parameters to Fix, Link Function, and Variance Estimation algorithms. You can also select various program options such as whether to list the Data, initialize parameter estimate values, compute profile likelihood confidence intervals for real parameter estimates, standardize individual covariates, specify what value of individual covariates will be used to compute the real parameters (real parameter estimates from individual covariates), plus other program options that concern the numerical optimization of the likelihood function to obtain parameter estimates. Use your tab key to highlight each option, and hit the F1 key to get help concerning what that option does. The MCMC checkbox allows you to use Bayesian methods to estimate the beta parameters.
If you opened the Run Window because you chose to run a Pre-Defined Model, a button is available to select which pre-defined models you want to run.
If you opened the Run Window to save the structure of the current model, you still need to select from the options available, but only the model structure will be added to the Results Browser. You can then run the model later with the Save Model Structure batch facility.
When you are happy with the values you have entered in the Run Window, you can click on the OK button to proceed with parameter estimation. Otherwise, you can click on the Cancel button to return to the model specification screens.
A set of Estimation Windows are opened as a separate execution thread to monitor the progress of the numerical estimation process. A summary of the results are reported in the visible window. You can minimize this estimation window (click on the - icon), and then proceed in MARK to develop specifications for another model to be estimated. When the estimation process is done, the estimation window will close, and a message box reporting the results and asking if you want to append them to the results database will appear as an icon at the bottom of your screen. Click on the icon to view the summary, and the OK button in the message box to append the results. Many, (I have had up to 6) estimation windows can be operating at once, and eventually, each will end and you will be asked if you want to append the results to the results database. If you end an estimation window prematurely by clicking on the X icon, the message box requesting whether you want to add the results will have mostly zero values. You would not want to append this incomplete model, so click No.