binner: Bin occurrences in geologic intervals

In brpetrucci/paleobuddy: Simulating Diversification Dynamics

Bin occurrences in geologic intervals

Description

Given a vector of fossil occurrences and time bins to represent geological ranges, returns the occurrence counts in each bin.

Usage

binner(x, bins)

Arguments

x	The vector containing occurrence times for one given species.
bins	A vector of time intervals corresponding to geological time ranges.

Details

The convention for couting occurrences inside a bin is to count all occurrences exactly in the boundary furthest from zero and exclude bins exactly in the boundary closest to zero. Then, in the bin closest to zero (i.e., the "last", or "most recent" bin), include all occurrence on each of the two boundaries. So occurrences that fall on a boundary are placed on the most recent bin possible

Value

A vector of occurrence counts for each interval, sorted from furthest to closest to zero.

Author(s)

Matheus Januario and Bruno do Rosario Petrucci

Examples

###
# first let us create some artificial occurrence data and check

# occurrence vector
x <- c(5.2, 4.9, 4.1, 3.2, 1, 0.2)

# bins vector
bins <- c(6, 5, 4, 3, 2, 1, 0)

# result
binnedSamp <- binner(x, bins)
binnedSamp

###
# it should work with any type of number in bins

# occurrence vector
x <- c(6.7, 5.03, 4.2, 3.4, 1.2, 0.4)

# bins vector
bins <- c(7.2, 6.7, 5.6, 4.3, 3.2, sqrt(2), 1, 0)

# result
binnedSamp <- binner(x, bins)
binnedSamp

###
# let us try with a real simulated species fossil record

# set seed
set.seed(1)

# run the simulation
sim <- bd.sim(1, lambda = 0.1, mu = 0.05, tMax = 15)

# sample it
sampled <- sample.clade(sim = sim, rho = 1, tMax = 15, S = 1)$SampT

# bins vector
bins <- c(15.1, 12.3, 10, 7.1, 5.8, 3.4, 2.2, 0)

# result
binnedsample <- binner(sampled, bins)
binnedsample

brpetrucci/paleobuddy documentation built on July 26, 2023, 8:15 p.m.