event_stretches: Find and Classify Unbroken Stretches of an Event

In rBatt/trawlDiversity: Long-term changes in species richness along the North American coastline

Description

Like, run length encoding (see rle), this function finds stretches of a vector that contain consecutive repeats of a particular value. This function then procedes by classifying each event in a stretch as being closer to the beginning or end of the stretch.

Usage

event_stretches(X)

Arguments

X	a data.table with columns for present, year, now_ext, col, and ext_dist_sign (see Details)

Details

The contents of the columns in X are as follows:

present	1 for event, 0 for non-event. "Streaks" refer to consecutive 1's
year	calendar year, or any time index indicating distance (space, time, etc) between events.
now_ext	"now extinct"; integer vector of 1 or 0. 1 indicates that present contains the first 0 following a streak of 1's
col	"colonization"; integer vector of 1 or 0. 1 indicates that present contains the first 1 at the beginning of a streak of 1's
ext_dist_sign	"signed distance to extinction"; output from event_distance; magntiude is distance in years to non-event, with negative numbers indicating that closest non-event is in past (post-colonization)

Value

Returns a named list of length 2: stretch_id and hybrid_part.

The values in stretch_id indicate the following:

-1	the stretch is an extinction-only stretch, which can only happen for a stretch at the beginning of a vector b/c the first element in present is 1, so there is no initial 0-to-1 transition
-2	colonization-only stretch; only occurs at end of vector where last value in present is 1 (no extinction)
1,2,...	a hybrid stretch, occurs for a stretch in present that is begun and terminated by a 0; this is the most generic case; the integer value serves to distinguish among multiple hybrid stretches

When the stretch is classified as a "hybrid", some of the 1's will be closer to the initial 0 than to the terminating 0. Those closer to the inital 0 are considered "post-colonization", whereas those closer to the final 0 are considered "pre-extinction". Proximiting is defined using year. Ties are ~arbitrarily attributed to post-coloniztion.

The values in hybrid_part indicate the following:

1	post-colonization
2	pre-extinction

rBatt/trawlDiversity documentation built on Aug. 14, 2021, 1:01 p.m.