is.overlapping: Test for self-overlap in a data.table or a pair of vectors

In kaufman-lab/intervalaverage: Time-Weighted Averaging for Interval Data

Test for self-overlap in a data.table or a pair of vectors

Description

is.overlapping tests whether a data.table contains intervals which partially or completely overlap with other intervals in different rows, possibly within groups. is.overlappingv tests whether intervals defined by a pair of vectors contains intervals which partially or completely overlap.

Usage

is.overlapping(x, interval_vars, group_vars = NULL, verbose = FALSE)

Arguments

x	A data.table with two columns defining closed intervals (see also interval_vars).
interval_vars	A length-2 character vector corresponding to column names of x which designate the closed (inclusive) starting and ending intervals. The column name specifying the lower-bound column must be specified first. these columns be of the same class and either be integer or IDate.
group_vars	NULL or a character vector corresponding to column names of x. overlap checks will occur within groups defined by the columns specified here.
verbose	prints additional information, default is FALSE

Details

These functions provide a fast check to see if any intervals in a set overlap. To actually identify specific segments of overlap, the data.table::foverlap can be use to return self-join for partial and/or exactly overlapping intervals.

intervalaverage::isolateoverlaps can be used to break partially overlapping intervals into separate intervals of exact overlap and non-overlap.

Note that it's also possible to use data.table::foverlap directly to test the existence of overlaps in a set of intervals (in fact, that's a what is.overlapping did in version 0.8.0 and before). However, this performs a join and if there are many overlaps then foverlaps will join them all–this is unnecessarily slow and memory intensive if the goal is to just test for the existence of one or more overlap.

Value

length-1 logical vector. TRUE if there are any overlaps, FALSE otherwise. (note that a single pair of overlapping intervals within a single group specified by group_vars will result in TRUE)

Examples

x <- data.table(start=c(1L,2L),end=c(3L,4L))
is.overlapping(x,c("start","end")) #the interval 1,3 overlaps with the interval 2,4

y <- data.table(start=c(1L,3L),end=c(2L,4L))
is.overlapping(y,c("start","end")) #the interval 1,2 doesn't overlap other intervals in y
z <- data.table(start=c(1L,3L,1L,2L),end=c(2L,4L,3L,4L),id=c(1,1,2,2))
is.overlapping(z,c("start","end"),"id")

#note the above returns TRUE because there is an overlap in the group defined by z$id==2
#to identify which group(s) are overlapping:

kaufman-lab/intervalaverage documentation built on Feb. 4, 2023, 9:19 a.m.