tgs_dist: Calculates distances between the matrix rows

In tgstat: Amos Tanay's Group High Performance Statistical Utilities

Calculates distances between the matrix rows

Description

Calculates distances between the matrix rows.

Usage

tgs_dist(x, diag = FALSE, upper = FALSE, tidy = FALSE, threshold = Inf)

Arguments

x	numeric matrix
diag	see 'dist' documentation
upper	see 'dist' documentation
tidy	if 'TRUE' data is outputed in tidy format
threshold	threshold below which values are outputed in tidy format

Details

This function is very similar to 'package:stats::dist'. Unlike the latter it uses all available CPU cores to compute the distances in a much faster way.

Unlike 'package:stats::dist' 'tgs_dist' uses always "euclidean" metrics (see 'method' parameter of 'dist' function). Thus:

'tgs_dist(x)' is equivalent to 'dist(x, method = "euclidean")'

'tgs_dist' can output its result in "tidy" format: a data frame with three columns named 'row1', 'row2' and 'dist'. Only the distances that are less or equal than the 'threshold' are reported. Distance between row number X and Y is reported only if X < Y. 'diag' and 'upper' parameters are ignored when the result is returned in "tidy" format.

Value

If 'tidy' is 'FALSE' - the output is similar to that of 'dist' function. If 'tidy' is 'TRUE' - 'tgs_dist' returns a data frame, where each row represents distances between two pairs of original rows.

Examples

# Note: all the available CPU cores might be used

set.seed(seed = 0)
rows <- 100
cols <- 1000
vals <- sample(1:(rows * cols / 2), rows * cols, replace = TRUE)
m <- matrix(vals, nrow = rows, ncol = cols)
m[sample(1:(rows * cols), rows * cols / 1000)] <- NA
r <- tgs_dist(m)

tgstat documentation built on July 9, 2023, 6:06 p.m.