SPARTAAS (version 1.2.4)

overlap: Temporal overlap index

Description

The overlap index is the ratio between internal overlap and total overlap over time. We define the limit of total overlap as: the minimum of the lower limits of the pair of individuals and the maximum of the upper limits. We define the internal overlap limit as the maximum of the lower limits and the minimum of the upper limits.

Usage

overlap(temporal)

Value

D

The dissimilarity matrix base on the overlap index.

Arguments

temporal

A data frame with tree columns: the name of the element, the lower limit and the upper limit.

Author

A. COULON

L. BELLANGER

P. HUSI

Details

The lower and upper limits must be numeric.

The dissimilarity between time periods is calculated as the ratio of the overlap of the time periods (distance in the case of disjoint time periods) to the cumulative extent of the two time periods.

As the ratio is bounded between -1 and 1, we add 1 to make it positive and normalise it so that it is between 0 and 1.

This overlap index then needs to be transformed into a dissimilarity index between sets. To do this we use the 1 - ratio. It is equal to 0 if the two time periods are identical and 1 if they are infinitely different.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
library(SPARTAAS)
data(dataceram)
dist <- overlap(dataceram$timerange)