:tocdepth: 3

.. _guppy_rarefy:

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rarefy
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`rarefy` performs rarefaction on collections of placements.

::

  usage: rarefy [options] placefile

Options
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-o  Specify the filename to write to.
--out-dir  Specify the directory to write files to.
--prefix  Specify a string to be prepended to filenames.
--seed  Set the random seed, an integer > 0. Default is 1.
-n  The number of pqueries to keep per placefile.
--weight-as-count  Interpret (integer) weights on pqueries as counts and sample without replacement.

Details
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Rarefaction *with replacement*, which is necessary because we allow floating point multiplicities.