Big Restructure and Cleanup of Pipeline

1. cleaned up existing pipeline, added package labels where applicable
2. implemented new aesthetic file formats
3. increased flexibility towards other assay designs
4. reduced complexity of calculation steps, increased calculation speed
5. implemented the ability to handle an additional variable, not only different concentrations (i.e. now able to handle different fish lines or microbial statuses AND different concentrations)
6. implemented the ability to handle custom survival categories and quantify them