jPAP Manual > III. Analysis Commands
Before any of the commands on the Command Menu of the Project Window are available for execution, Pedigree and Observation Documents must be prepared, metadata must be defined, and at least one genetic model defined. To provide a motivational context for the preparatory tasks detailed in subsequent chapters, this chapter provides an overview of command execution and details the commands available.
Upon selecting a command from the Command Menu, it executes immediately. Commands may be executed concurrently if desired. Every command option produces some sort of report, which appears in the PAReporter under its own tab. Some commands also update the genetic model; the updated model will appear under a new tab in ModEd upon successful execution.
When a command is launched, it uses the settings on the main form of the Project Window and in the four documents to which it points. It will also use any settings in the Project Window's extended form that apply to it in the context of the main settings. If the purpose of an extended setting is not clear, additional information may be obtained by placing the mouse over its field label. It is recommended that you obtain an overview of the extended settings by this means; the main settings are discussed in detail in other chapters.
The Command Menu organization groups the options logically. Most options involve computation over pedigrees of an objective function F. Typically F is the likelihood, but an alternative objective function (lod score or chi-square statistic, depending on context) may be specified for some commands using the extended settings. Commands involving F further subdivide into those which compute F over specific parameter values, and those which search the parameter space for an optimal F. Commands in the former group will be collectively referred to herein as "survey" commands, while the latter will be called "search" commands. After describing each of these command groups in turn, this chapter concludes with a discussion of the "specialized" commands that do not compute F.