Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/1003clusterJarvisPatrick.R
Nearest Neighbors
1  NNeighbors(x, numNbrs = NULL, cutoff = NULL, ...)

x 
Either an 
numNbrs 
Number of neighbors to find for each item. If not enough neighbors can be found the matrix will be padded with NA. 
cutoff 
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 numNbrs
or cutoff
should be given, cutoff
will take precedence if both are given. If numNbrs
is
given, then that many neighbors will be returned for each item in the set. If cutoff
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 cutoff
is
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
Minfeng Zhu <wind2zhu@163.com>
See clusterJP
for JarvisPatrick Clustering
1 2 3  data(sdfbcl)
apbcl = convSDFtoAP(sdfbcl)
nnm = NNeighbors(apbcl, cutoff = 0.5)

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