Diversity Functions

This code is designed to help process files output from the sequence anlaysis software mothur. The typical user will go from raw sequence data to a shared files using the program mothur. The next steps include using the shared file to generate a taxa-by-site matrix that can be used to test hypotheses. This code now only provides R fucntions to create taxa-by-site matrices, but also contains functions to perform basic diversity measures. This code represents the beta version of my ideas for properly analyzing microbial community data. If you would like to join the discussion, please feel free to email me.