nnt: Nearest Neighbour Search with Variables on a Torus

Description Usage Arguments Details Value References See Also Examples

View source: R/nearest_neighbours_on_a_torus.R

Description

Uses a user-supplied function to find the k nearest neighbours of specified points in a dataset, adding the option to wrap certain variables on a torus.

Usage

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nnt(data, query = data, k = min(10, nrow(data)), fn = RANN::nn2,
  torus, ranges, method = 1, ...)

Arguments

data

An M by d numeric matrix or data frame. Each of the M rows contains a d-dimensional observation.

query

An N by d numeric matrix or data frame. Each row contains an d-dimensional point that will be queried against data.

k

An integer scalar. The number of nearest neighbours, of the points in the rows of query, to find.

fn

The function with which to calculate the nearest neighbours. The syntax of this function must be fn(data, query, k, ...). The default is RANN::nn2. Other possibilities are RANN.L1:nn2 and nabor::knn.

torus

An integer vector with element(s) in {1, ..., ncol(data)}. The corresponding variables are wrapped on the corresponding range gives in ranges.

ranges

A length(torus) by 2 numeric matrix. Row i gives the range of variation of the variable indexed by torus[i]. ranges[i, 1] and ranges[i, 2] are equivalent values of the variable, such as 0 degrees and 360 degrees. If length(torus) = 1 then ranges may be a vector of length 2.

method

An integer scalar, equal to 1 or 2. See Details.

...

Further arguments to be passed to fn.

Details

If method = 1 then the data are partially replicated, arranged around the original data in a way that wraps the variables in torus on their respective ranges in ranges. Then fn is called using this replicated dataset as the argument data. If k is large and/or data is a sparse dataset then it is possible that a single observation contributes more than once to a set of nearest neighbours, which is incorrect. If this occurs then nnt uses method 2 to correct the offending rows in nn.idx and nn.dists in the returned list object.

If method = 2 then the following approach is used for the point in each row in query. The data indexed by torus are shifted (and wrapped) so that the point is located at the respective midpoints of ranges. Method 2 is efficient only if the number of points in query is small.

If torus is missing then fn is called using fn(data = data, query = query, k = k, ...), so that a call to nnt is equivalent to a call to the function chosen by fn.

Value

An object (a list) of class c("nnt", "donut") containing the following components.

nn.idx

An N by d integer matrix of the k nearest neighbour indices, i.e. the rows of data.

nn.dists

An N by d numeric matrix of the k nearest neighbour distances.

data, query, k, fn

The arguments data, query, k and fn (in fact substitute(fn)).

torus, ranges, method

If torus is supplied, the arguments torus, ranges and method.

call

The call to spm.

References

Arya, S., Mount, D., Kemp, S. E. and Jefferis, G. (2019) RANN: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric. R package version 2.6.1. https://CRAN.R-project.org/package=RANN

Arya, S., Mount, D., Kemp, S. E., Jefferis, G. and Muller, K. (2018) RANN: Fast Nearest Neighbour Search (Wraps ANN Library) Using L1 Metric. R package version 2.5.2. https://CRAN.R-project.org/package=RANN.L1

Elseberg J., Magnenat S., Siegwart R., Nuchter, A. (2012) Comparison of nearest-neighbor-search strategies and implementations for efficient shape registration. Journal of Software Engineering for Robotics (JOSER), 3(1), 2-12 https://CRAN.R-project.org/package=nabor

See Also

RANN::nn2, RANN.L1::nn2, nabor::knn: nearest neighbour searches.

plot.nnt plot method for objects returned from nnt (1 and 2 dimensional data only).

Examples

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got_RANN <- requireNamespace("RANN", quietly = TRUE)
got_RANN.L1 <- requireNamespace("RANN.L1", quietly = TRUE)
got_nabor <- requireNamespace("nabor", quietly = TRUE)

set.seed(20092019)
# 2D example from the RANN:nn2 documentation (L2 metric)
x1 <- runif(100, 0, 2 * pi)
x2 <- runif(100, 0, 3)
DATA <- data.frame(x1, x2)
if (got_RANN) {
  nearest <- nnt(DATA, DATA)
}

# Suppose that x1 should be wrapped
ranges1 <- c(0, 2 * pi)
query1 <- rbind(c(6, 1.3), c(2 * pi, 3), c(3, 1.5), c(4, 0))
if (got_RANN) {
  res1 <- nnt(DATA, query1, k = 8, torus = 1, ranges = ranges1)
  plot(res1, ylim = c(0, 3))
}

# Suppose that x1 and x2 should be wrapped
ranges2 <- rbind(c(0, 2 * pi), c(0, 3))
query2 <- rbind(c(6, 1.3), c(2 * pi, 3), c(3, 1.5), c(4, 0))
if (got_RANN) {
  res2 <- nnt(DATA, query2, k = 8, torus = 1:2, ranges = ranges2)
  plot(res2)
}

# Use nabor::knn (L2 metric) instead of RANN::nn2
if (got_nabor) {
  res3 <- nnt(DATA, query2, k = 8, fn = nabor::knn, torus = 1:2,
              ranges = ranges2)
  plot(res3)
}

# Use RANN.L1::nn2 (L1 metric)
if (got_RANN.L1) {
  res4 <- nnt(DATA, query2, k = 8, fn = RANN.L1::nn2, torus = 1:2,
              ranges = ranges2)
  plot(res4)
}

# 1D example
ranges <- c(0, 2 * pi)
query <- c(4, 0.1)
if (got_RANN) {
  res <- nnt(x1, query, torus = 1, ranges = ranges, method = 1)
  plot(res)
}

donut documentation built on Oct. 6, 2019, 5:06 p.m.