get_colonizers: Get Colonizations and Extinctions

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

Description

Identify species colonizing, going extinct, and persisting between years

Usage

get_colonizers(d)

Arguments

d	An input data.table with columns spp, year, stratum, haulid, depth, lon, lat (may have others, but they aren't used)

Value

A list of length 5:

col_dt	colonization events for each year-stratum-species.
col_ext_dt	colonization (1), extinction (-1), or no change for each species-year
n_cep	the number of colonizations, extinctions, or no-change events in the whole region for each year
n_spp_col_weighted	appropriate aggregation of the column by this name in col_dt
n_spp_col_weighted_tot	like n_spp_col_weighted, but summed up across years (and divided by yrs_sampled)

Note that for each element with "col" in its name, there is an extinction counterpart; i.e., ext_dt, n_spp_ext_weighted, n_spp_ext_weighted_tot.

The columns in col_dt (or ext_dt for extinction equivalent) are:

col_logic	logical indicating year-stratum-spp colonization (name is still col_logic in ext_dt)
n_spp_col	number of species that colonized a stratum in a year
n_strat_col	number of strata colonized by this specie sin this year
n_spp_col_weighted	Like n_strat_col, but divided by n_strat_col (e.g. if a species colonizes 5 strata, it only contributes 0.2 to each stratum).
yrs_sampled	The number of years a stratum was sampled.

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