The analysis begins with a series of matrices representing different moments in time (e.g., years). The matrices are brought into Pajek in chronological order and consecutively saved as mtrx1.net, mtrx2.net, etc., using the standard Pajek-format (edgelist).
This set of matrices is to be saved in a folder together with the program mtrx2paj.exe. We need this program in order to make a step which cannot be made within the Pajek environment. Mtrx2Paj.Exe can best be run within a DOS box because in that case one receives error messages if something goes wrong, but it will work also when clicked directly from Windows. (A similar program for bi-modal matrices is available from here, as bimodal.exe.)
A screen should open prompting the user for the number of files (mtrx1.net, mtrx2net, etc.). Each file is now considered as a time instant and a file is written (potentially overwritten) with the name pajek.net. This file contains the time indicators needed by Pajek for generating a comprehensive project file which contains all the necessary information for Visone. (The file pajek.net is also compatible with the input requirements of the program SoNIA: Social Network Image Animator.)
Pajek.net is read into Pajek using File > Network > Read. It is easiest to make global changes to the file at this stage. For example, one may wish to convert all arcs into edges in order to prevent double arrows in the animations (Net > Transform > All Arcs to Edges), etc. One may also wish to set a threshold value for the lines (Net > Transform > Remove). Once the file is thus set, it is best to export the file once more with a different name (e.g., pajek2.net), restart Pajek, and reimport it so that it is the first network in the list.
Net > Transform > Generate in time! A set of networks is now available. The set can be saved as a Pajek project file under File > Pajek project. The file has the extension .paj and can directly be read by Visone under Dynamic > Import Dynamic Pajek. (Alternatively, one can use this file for animations using PajekToSVGAnim.Exe, but in this case one may wish to run Kamada-Kawai in each of the networks with reference to the previous solution.)
Within Visone, first use the analysis mode (View > Mode). Click the second-right button in the taskbar to toggle aggregation view. Layout > Uniform if you wish to delete isolates. You can select them with the mouse and delete them thereafter.
Optimize the properties for the nodes and links. First select all nodes and links under Edit > Select all. Set the node sizes under Nodes > Properties; for example, width and height to 30.0. You can also change the label settings, for example choose Model > 8 Pos. Using this setting the label will appear above the node. And if so wished, one can also change the font size. The properties for the links are found under Links > Properties.
Deselect all nodes and links. Undo the aggregation by clicking again on the second-right button. Perform the statistical analyses (e.g., centrality measures) using the Analysis tab in the left-hand pane. If so wished, run the additional options for under Dynamic. Choose the settings for the Visualization, and set the options under File > Options > Dynamic. For instance, deselect Rezoom Animation under the Dynamic tab.
Open the dynamic layouter (Layout > Dynamic). Select under option level “expert”, and choose the desired parameter settings. For example, one can set the Stability to 4.0, Link Length to 200.0, Component Seperation to 0.6, and select Export Stress Values. Run “Layout”. View > Fit network. By clicking on the third-right button on the taskbar the animation can be toggled on/off.