How to use the Matrix Visualization - State Ordering

To use the Matrix Visualization - State Ordering, choose the Analytical Model Solution button, and then, the View Matrix button. The interface is shown in Figure .

Figure: The Matrix Visualization - States Permutation Interface.

The main options of the Matrix Visualization - State Ordering interface are :

1. Ordering of States
   • . This option is used when we want to see the structure of the matrix with the permutation of the state variables that is defined in the List of State Variables box. When we want to see the structure of the matrix after the chain is generated (the matrix visualization program does not guarantee any pre-defined state ordering), we do not select this option.
   • List of State Variables. Used to obtain a . The number on the left side of each variable represents its current position in the variable vector. It is possible to change the order of the variables with the following buttons: First, Up, Down, Last. The state variables are used to obtain a specific . For example, if the state variables are ordered as shown in Figure , then the states are ordered in such a way that the last state variable varies faster than the previous state variable, in increasing order. The tool generates the uniformized state transition probability matrix from the generator matrix.
2. Color Options. This option is used to associate colors to probabilities of states (Low, High and Zero probabilities). All the colors can be chosen from the following set black, white, red, green, blue, yellow, cyan, purple. The color depth defines the number of colors used to represent the probabilities. For example, if color depth is 4 then the number of colors used is $2^{4}=16$.
3. Extra Options
   • Use another extension to define the state transition probability matrix file. A new extension is used for the probability matrix file instead of the default
     $i$<model name>.st_trans_prob_mtx.
   • . This option is useful when the number of elements in the matrix is greater than the number of pixels in the window canvas.
     • Maximum Probability: the probability shown will be the maximum probability (in the transitions that occupy the pixel).
     • Minimum Probability: the probability shown will be the minimum probability (in the transitions that occupy the pixel).
     • Average Probability: the probability shown will be the average probability (in thetransitions that occupy the pixel).
   • Buttons
     • Show with the configurations specified in the interface.
     • Update Generates new files (generator matrix, etc) according to the new state ordering.
     • Close Closes the window.

The interface to visualize the matrix is shown in Figure .

Figure: The Matrix Visualization Interface.

The main options of the Matrix Visualization interface are:

• On the left, the matrix is shown.
• The displays information concerning the current zoom. There are options to zoom to a specific area of the matrix. The given parameters are the coordinates and the size of the area (in number of states).
• The tool bars are on the upper right corner. It is possible to choose among the following options: . The option Show Blocks: On/Off is used to show the blocks defined for the matrix and that will be used in block solution methods (e.g. GTH Block).
• The Block Information option allows the definition of matrix blocks. The user has to specify the initial state of a block, the size of a block and the total number of blocks with this size. The button Generate Output generates a file with (the extension of this file is .blocks). This file will be used as input for a solution method based on the block elimination (e.g. block GTH).