prorate.unidentified

dht.results

a list of character vectors detailing the 
species codes associated with the unidentified code given as the element 
name.

species.code.definitions

a list of character vectors defining the species
present in each strata.

species.presence

boolean whether observations are clusters of individuals
of identified species codes corresponding to which species are present in 
each strata.

clusters

The prorating is done individually for each strata. It will prorate the 
unidentified abundance between the species as defined in the
species.code.definitions except where specified that a given species is not 
present in that strata as defined in the species.presence argument.

Performs distance sampling analyses on a number of species
at once and can account for unidentified sightings, model uncertainty
and covariate uncertainty. Unidentified sightings refer to sightings
which cannot be allocated to a single species but may instead be
allocated to a group of species. The abundance of each unidentified
group is estimated and then prorated to the species estimates. Model
uncertainty should be incorporated when multiple models give equally
good fit to the data but lead to large differences in estimated
density / abundance. Covariate uncertainty should be incorporated
when covariates cannot be measured accurately, for example this is
often the case for group size in marine mammal surveys. Variance
estimation for these methods is via a non parametric bootstrap.
The methods implemented are described in Gerodette T. and Forcada
J. (2005) <doi:10.3354/meps291001> Non-recovery of two spotted and
spinner dolphin populations in the eastern tropical Pacific Ocean.

prorate.unidentified: Prorate the estimated abundances of the unidentified sightings to the other identified species categories.

Description

Usage

Arguments

Value