nearestNeighbors {ChemmineR} | R Documentation

## Nearest Neighbors

### Description

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.

### Usage

       nearestNeighbors(x, numNbrs = NULL, cutoff = NULL, ...)

### Arguments

`x` | Either an FPset or an APset.
`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 `numNbrs`. This parameter allows to obtain tighter clustering results.
`...` | These parameters will be passed into the distance function used, either `cmp.similarity` or `fpSim`, for APset and FPset, respectively.

### Value

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

### Author(s)

Kevin Horan

### See Also

`jarvisPatrick` `trimNeighbors`

### Examples

       data(sdfsample)
       ap = sdf2ap(sdfsample)
       nnm = nearestNeighbors(ap,cutoff=0.5)
       clustering = jarvisPatrick(nnm,k=2,mode="a1b")

[Package ChemmineR version 3.40.0 Index]