RAD-filtering =============  !!Work under progress: this repository does not contain all its components to work properly yet.  Disclaimer: I am not a programmer or a statistician. I just use R to filter and analyse my data to the best of my knowledge.  Also I have not been using R for a long time (started in Sept. 2012) which meanst that you can clearly see an evolution in the quality of the scripts. Some of the early scripts are long and inefficient (but work!), although some of them I have recently cleaned up to some extent. This means that some of the comments are rather elementary (they were meant for me as I was learning R) which may not be a bad thing as also users less familiar with R should be able to understand how the scripts work, and learn from them.  This Repository includes scripts that are used to filter STACKS output data (Catchen et al, 2011, G3: Genes, Genomes, Genetics).   It will include both the scripts with some comments and instructions on how to use them, and pipelines of worked examples with my own data (these will include the word "pipeline", the data files will include the work "data").  I have tried to make them userfriendly and added some flags and flexibility to the scirpts but as always your data will be unique and you may have to modified the original codes to make them work. People with some knowledge of R scripting should be able to do this easily.  If you are not that familiar with R, most of the time when my scripts don't work it hast to do with the fact that your data is wrongly formatted. The best thing to do is to compare your data with my worked example.  The scripts in this project can be used and changed by everyone so long as any changes are made available to everyone under the same conditions.