DOI: 10.5061/dryad.9zw3r229w
title: Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales

description: Effective conservation and management of animal populations requires
 knowledge of abundance and trends. For many species, these quantities are
 estimated using systematic visual surveys. Additional individual-level
 data are available for some species. Integrated population modelling (IPM)
 offers a mechanism for leveraging these datasets into a single estimation
 framework. IPMs that incorporate both population- and individual-level
 data have previously been developed for birds, but have rarely been
 applied to cetaceans. Here, we explore how IPMs can be used to improve the
 assessment of cetacean populations. We combined three types of data that
 are typically available for cetaceans of conservation concern:
 population-level visual survey data, individual-level capture-recapture
 data, and data on anthropogenic mortality. We used this IPM to estimate
 the population dynamics of the Cook Inlet population of beluga whales
 (CIBW; Delphinapterus leucas) as a case study. Our state-space IPM
 included a population process model and three observational submodels: 1)
 a group detection model to describe group size estimates from aerial
 survey data; 2) a capture-recapture model to describe individual
 photographic capture-recapture data; and 3) a Poisson regression model to
 describe historical hunting data. The IPM produces biologically plausible
 estimates of population trajectories consistent with all three datasets.
 The estimated population growth rate since 2000 is less than expected for
 a recovering population. The estimated juvenile/adult survival rate is
 also low compared to other cetacean populations, indicating that low
 survival may be impeding recovery. This work demonstrates the value of
 integrating various data sources to assess cetacean populations and serves
 as an example of how multiple, imperfect datasets can be combined to
 improve our understanding of a population of interest. The model framework
 is applicable to other cetacean populations and to other taxa for which
 similar data types are available.
description: /Data/CIBW_RSideCapHist_McGuire&Stephens.csv contains a
 matrix of right side capture histories (1 = captured, 0 = not captured)
 for each individual (rows) and year (columns).  Photographic
 capture-recapture data were collected by Tamara McGuire. These data are
 made available here, without restriction, but anyone wishing to use these
 data is requested to contact tamaracookinletbeluga@gmail.com,
 who can provide further information on how raw data were processed to
 provide capture histories.
 /Data/CIBW_HuntData_Mahoney&Shelden2000.xlsx contains the
 minimum documented number of animals killed (MinKilled) for years between
 1950 and 1998 as published in Mahoney and Shelden 2000.  Entries which are
 NA indicate that no data were available for that year. 
 /Data/CIBW_Abundance_HobbsEtAl2015.xlsx contains the total group
 size estimates from Hobbs et al. 2015.
 /Data/CIBW_Abundance_BoydEtAl2019.txt contains an array with
 dimensions [1:1000, 1:8, 1:11] containing 1000 posterior samples of total
 group size for up to 8 survey days over 11 years, as described in Boyd et
 al. 2019.  
description: Models/CIBW_IPM_BetaPObs.txt contains the JAGS model
 specification as presented in Appendix Data S1.  
 Scripts/CIBW_01_CalcPObs.R provides the scripts used to calculate
 the scale and shape parameters of the beta distribution used as a prior
 for the probability of observing belugas, as described in Appendix
 S1. Scripts/CIBW_02_LoadData.R includes code for
 reading in and formatting data prior to modeling.
 Scripts/CIBW_03_RunModel.R runs the Bayesian model using jagsUI
 and outputs an RData object.