Adds prune argument to control handling of undirected (symmetric) matrices #4
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Parameters added "prune" and "directed" for compatibility with an R implementation of a Python library (dependent on the Python implementation of PhenoGraph). See the following Python version where these parameters have been documented:
https://github.com/jacoblevine/PhenoGraph/blob/master/phenograph/cluster.py
Minor changes have been made to the documentation and error messages.
Note that this changes the outputs of the algorithm. The default behaviour of the function has been changed for consistency with the Python version. This is a proposed change for consideration only as it may not be backwards-compatible with Rphenograph version 0.99.1.