R/nn.R In swaRm: Processing Collective Movement Data

Documented in nnnndpdist

```#' @title Pairwise Distance Matrix
#'
#' @description Given a set of locations, this function computes the distances
#'  between each possible pair of locations.
#'
#' @param x A vector of x (or longitude) coordinates.
#'
#' @param y A vector of y (or latitude) coordinates.
#'
#' @param geo A logical value indicating whether the locations are defined by
#'  geographic coordinates (pairs of longitude/latitude values). Default: FALSE.
#'
#' @return A square matrix representing pairwise distances between each possible
#'  pair of locations.
#'
#' @author Simon Garnier, \email{garnier@@njit.edu}
#'
#'
#' @examples
#' x <- rnorm(25)
#' y <- rnorm(25, sd = 3)
#' pdist(x, y)
#'
#' @export
pdist <- function(x, y, geo = FALSE) {
if (length(x) != length(y))
stop("x and y should have the same length.")

if (!is.numeric(x) | !is.numeric(y))
stop("x and y should be numeric.")

if (geo) {
l <- length(x)
idx <- expand.grid(row = 1:l, col = 1:l)
m1 <- cbind(x[idx\$row], y[idx\$row])
m2 <- cbind(x[idx\$col], y[idx\$col])
matrix(geosphere::distGeo(m1, m2), nrow = l, ncol = l)
} else {
as.matrix(stats::dist(cbind(x, y)))
}
}

#' @title Nearest Neighbor
#'
#' @description Given the locations of different objects, this function
#'  determines the identity of the nearest neighboring object to each object.
#'
#' @param x A vector of x (or longitude) coordinates.
#'
#' @param y A vector of y (or latitude) coordinates.
#'
#' @param id A vector corresponding to the unique identities of each track.
#'
#' @param geo A logical value indicating whether the locations are defined by
#'  geographic coordinates (pairs of longitude/latitude values). Default: FALSE.
#'
#' @return A vector of the same length as x and y representing the identity of
#'  the nearest neighboring object to each object.
#'
#' @author Simon Garnier, \email{garnier@@njit.edu}
#'
#'
#' @examples
#' x <- rnorm(25)
#' y <- rnorm(25, sd = 3)
#' id <- 1:25
#' nn(x, y, id)
#'
#' @export
nn <- function(x, y, id, geo = FALSE) {
if (!all(length(x) == c(length(y), length(id))))
stop("x, y and id should have the same length.")

if (!is.numeric(x) | !is.numeric(y))
stop("x and y should be numeric.")

d <- pdist(x, y, geo = geo)
diag(d) <- NA
d[is.na(x) | is.na(y), ] <- NA
d[, is.na(x) | is.na(y)] <- NA

idx <- apply(d, 2,
function(x) {
if (sum(is.na(x)) != length(x)) {
which(x == min(x, na.rm = TRUE))[1]
} else {
as.numeric(NA)
}
})
id[idx]
}

#' @title Nearest Neihgbor Distance
#'
#' @description Given the locations of different objects, this function
#'  determines the distance of the nearest neighboring object to each object.
#'
#' @param x A vector of x (or longitude) coordinates.
#'
#' @param y A vector of y (or latitude) coordinates.
#'
#' @param geo A logical value indicating whether the locations are defined by
#'  geographic coordinates (pairs of longitude/latitude values). Default: FALSE.
#'
#' @return A vector of the same length as x and y representing the distance to
#'  the nearest neighboring object for each object.
#'
#' @author Simon Garnier, \email{garnier@@njit.edu}
#'
#'
#' @examples
#' x <- rnorm(25)
#' y <- rnorm(25, sd = 3)
#' id <- 1:25
#' nnd(x, y)
#'
#' @export
nnd <- function(x, y, geo = FALSE) {
if (length(x) != length(y))
stop("x and y should have the same length.")

if (!is.numeric(x) | !is.numeric(y))
stop("x and y should be numeric.")

d <- pdist(x, y, geo = geo)
diag(d) <- NA
d[is.na(x) | is.na(y), ] <- NA
d[, is.na(x) | is.na(y)] <- NA

apply(d, 2,
function(x) {
if (sum(is.na(x)) != length(x)) {
min(x, na.rm = TRUE)
} else {
as.numeric(NA)
}
})
}
```

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swaRm documentation built on Jan. 11, 2023, 5:19 p.m.