nearestNeighbors: nearestNeighbors

In insilico/npdr: Nearest-neighbor Projected-Distance Regression

nearestNeighbors

Description

Find nearest neighbors of each instance using relief.method Used for npdr (no hits or misses specified in neighbor function).

Usage

nearestNeighbors(
  attr.mat,
  nbd.method = "multisurf",
  nbd.metric = "manhattan",
  sd.vec = NULL,
  sd.frac = 0.5,
  k = 0,
  neighbor.sampling = "none",
  att_to_remove = c(),
  fast.dist = FALSE,
  dopar.nn = FALSE
)

Arguments

attr.mat	m x p matrix of m instances and p attributes, or m x m distance matrix if metric is 'precomputed'
nbd.method	neighborhood method 'multisurf' or 'surf' (no k) or 'relieff' if you want to specify k (required k).
nbd.metric	used in npdrDistances for distance matrix between instances. parameter can be 'precomputed' if user-supplied distance matrix. default to 'manhattan' (numeric input).
sd.vec	vector of standard deviations for surf
sd.frac	multiplier of the standard deviation from the mean distances, subtracted from mean distance to create for SURF or multiSURF radius. The multiSURF default "dead-band radius" is sd.frac=0.5: mean - sd/2
k	number of constant nearest hits/misses for "relieff" (fixed k). The default k=0 means use the expected SURF theoretical k with sd.frac (.5 by default) for relieff nbd.
neighbor.sampling	"none" or "unique" if you want to return only unique neighbor pairs
att_to_remove	attributes for removal (possible confounders) from the distance matrix calculation.
fast.dist	whether or not distance is computed by faster algorithm in wordspace, default as F
dopar.nn	whether or not neighborhood is computed in parallel, default as F

Value

Ri_NN.idxmat, matrix of Ri's (first column) and their NN's (second column)

Examples

# multisurf neighborhood with sigma/2 (sd.frac=0.5) "dead-band" boundary
neighbor.pairs.idx <- nearestNeighbors(
  predictors.mat,
  nbd.method = "multisurf",
  nbd.metric = "manhattan",
  sd.frac = 0.5
)
head(neighbor.pairs.idx)

# reliefF (fixed-k) neighborhood using default `k` equal to
# theoretical surf expected value.
# One can change the theoretical value by changing sd.frac (default 0.5).
neighbor.pairs.idx <- nearestNeighbors(
  predictors.mat,
  nbd.method = "relieff",
  nbd.metric = "manhattan"
)
head(neighbor.pairs.idx)

# reliefF (fixed-k) neighborhood with a user-specified k
neighbor.pairs.idx <- nearestNeighbors(
  predictors.mat,
  nbd.method = "relieff",
  nbd.metric = "manhattan",
  k = 10
)
head(neighbor.pairs.idx)

insilico/npdr documentation built on July 6, 2023, 1:14 p.m.