10.5061/DRYAD.5SR24
Foote, Michael
University of Chicago
Data from: On the measurement of occupancy in ecology and paleontology
Dryad
dataset
2016
occupancy
sampling
Phanerozoic
Metazoa
2020-07-05T00:00:00Z
en
https://doi.org/10.1017/pab.2016.24
8952 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Occupancy statistics in ecology and paleontology are biased upward by the
fact that we generally do not have solid data on species that exist but
are not found. The magnitude of this bias increases as the average
occupancy probability decreases and as the number of sites sampled
decreases. A maximum-likelihood method is developed to estimate the
underlying distribution of occupancy probabilities of all species based
only on the sample of observed species with nonzero occupancy. The method
is based on determining the probability that the number of occupied sites
will take on any specific value for a given occupancy probability,
integrated over the entire distribution of occupancy probabilities. If the
shape of the underlying distribution is well modeled, the resulting
occupancy estimates circumvent the bias inherent in failing to observe
some species and the fact that this bias depends on the number of sites.
For occupancy data on marine animal genera drawn from the Paleobiology
Database, the underlying distribution is reasonably approximated as a
right-truncated log-normal, but the methods developed can be extended to
any distribution. Examples are presented to illustrate some observations
that are robust and others that need to be revised in light of this bias
correction. The method is compared to a recently developed,
distribution-free approach to the same problem.
R scripts for maximum-likelihood estimation of occupancy
distributionsR_Scripts.R
Global