Number of neighbors to find for each item. If not enough neighbors can be found the matrix will be padded with NA.
The minimum similarity value an item must have to another item in order to be included
in that items neighbor list. This parameter takes precedence over
These parameters will be passed into the distance function used
Computes the nearest neighbors of descriptors in an FPset or APset object for use with the
jarvisPatrick clustering function. Only one of
should be given,
cutoff will take precedence if both are given. If
given, then that many neighbors will be returned for each item in the set. If
is given, then, for each item X, every neighbor that has a similarity value greater than or
equal to the cutoff will be returned in the neighbor list for X.
The return value is a list with the following components:
indexes - index values of nearest neighbors, for each item. If
used, this will be a list of lists, otherwise it will be a matrix
names - The names of each item in the set, as returned by cid
similarities - The similarity values of each neighbor to the item for that row.
This will also be either a list of lists or a matrix, depending on whether or not
cutoff was used. Each similarity values corresponds to the id number in the
same position in the indexes entry
Min-feng Zhu <email@example.com>
clusterJP for Jarvis-Patrick Clustering
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