check.species.code.definitions

a list with an element for each 
unidentified code which contains a vector of corresponding identified 
species codes or NULL if not required

species.code.definitions

a vector of species names for which model names were 
supplied in the ddf.models list passed to execute.multi.analysis by the 
user.

species.name

Firstly, it checks that there are not multiple definitions for the same species code.
Secondly, it checks that the names of the ddf models correspond to the names 
in the species code definitions. Lastly, it checks that definitions are 
provided for all species codes and if not it adds the missing definitions 
assuming they correspond to identified categories

internal

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.

check.species.code.definitions: Checks the list of species code definitions supplied by the user

Description

Usage

Arguments

Value

See Also