Starting MDS  MDS SETUP 
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When Nonmetric MDS is selected, the MDS Setup dialog is activated.
Initial Start Position This is a radio button selection. Select PCA to use a Principal Coordinates Analysis (note, this is not the same as a Principal Component Analysis) to calculate the starting coordinates of the sites (columns). Select Random to use a random number generator to assign initial coordinates. The default is to use a PCA. The algorithm used by CAP to find the final coordinates will produce different results depending upon the starting configuration. Indeed, a poor initial choice may result in the algorithm becoming trapped before a low stress value is reached. Generally, PCA will produce a satisfactory choice. It is often useful to undertake a few runs with random starting points to satisfy yourself that the algorithm is finding a minimumstress solution.
Rotate output. Select Yes or No by clicking on the radio buttons. If Yes is selected a PCA is performed on the final site coordinates. The default is Yes, as this will usually produce the most suitable plot.
Similarity measures. The measure to use is selected by clicking on the radio button. A number of different measures can be used to calculate the distances between sites. The regular options available are Euclidean distance, Sorensen, Jaccard and Bray Curtis.The default is Bray Curtis. If you prefer, tick the 'Other measure' box and select any of the other similarity measures offered by CAP.
Number of dimensions. This is a slider bar activated by the mouse. The default value is 2. If a higher number is chosen, the program will calculate the configuration of the points from this dimension down to 1 dimension, list the final stress for each number of dimensions under the Stress tab, and display the change in the stress value with number of dimensions graphically. The coordinates of the points for the maximum number of dimensions are displayed under the Sample coordinates tab. However, the plot of the positions of the site is that found for a twodimensional space.
Maximum iterations. You can change the number of iterations used by the stress minimisation algorithm by using the mouse to move the slider bar. The default is 200. While there is a relationship between the number of iterations and the magnitude of the stress level achieved, in practice there is often little advantage in selecting a higher iteration number. You may like to vary this number to become satisfied that the minimum stress level possible has been achieved.
