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Start CAP in the normal Windows fashion either by clicking on the Desktop icon or from Start: All Programs: CAP 5.
Along the top bar are a number of drop-down menus. These work in the same way as other standard Windows programs.
File: To open, re-open, create, export, print and save data sets.
Edit: To cut copy and paste to and from the active window.
Ordination: To select an ordination method to apply to the data.
Twinspan: To initiate a Twinspan analysis.
Clustering: To select a cluster analysis.
Similarity: To display similarity measures between samples.
Association: To perform a Chi squared association test.
Group tests: To assign samples to groups and look for similarities between the groups.
Experimental: To use the experimental Species Filtering method.
Compare: To compare samples in terms of the variables present.
Help: to enter the Help system.
When the program is started, you will be presented with a blank working area. Use File: Open or Reopen to select and open your data file, or File: New to create a new data set. The raw data will be displayed on the 'Raw data' page; there is a corresponding 'Working data' page where you can manipulate and transform the data. Initially, the Raw Data and Working Data will display the same values – except that CAP will remove any zero-sum rows or columns from the Working Data array. Once a transformation or some other adjustment has been applied to the data (for details see below) the Working Data form will display the adjusted data. The analyses will only use the Working Data set; your original (Raw) data will be unchanged, unless you choose to save the transformed data set over the existing file.
For more information about using CAP and a video demonstration see the Help: Guides: Introduction.