|
Stock
assessment of tunas
In collaboration with George Watters, Mark developed the
A-SCALA
(681 Kb) stock assessment model that is used
to assess tunas in the EPO by the IATTC. A-SCALA is a
statistical catch-at-length analysis based on the
MULTIFAN_CL stock assessment model (http://www.multifan-cl.org/).
Mark is continually updating the A-SCALA model (e.g.
http://www.spc.int/OceanFish/Html/SCTB/SCTB16/mwg2.pdf).
For several years Mark has been collaborating with
scientists from the Secretariat of the Pacific Community
(http://www.spc.org.nc/oceanfish/)
and the National Research Institute of Far Seas
Fisheries (NRIFSF) of Japan on a Pacific wide assessment
of bigeye tuna using MULTIFAN_CL (http://www.spc.int/OceanFish/Html/WCPFC/SC1/pdf/SC1_SA_WP_2_SUP.pdf).
Mark is also a main contributor to the PFRP Changes in
the Biomass of Large Pelagic Predators
Page (http://www.soest.hawaii.edu/PFRP/large_pelagics/large_pelagic_predators.html)
that counters misinterpretation of data. Several of his
presentations are available on that web site. |
|
. |
. |
A general framework for modeling protected species
Mark has obtained funding
from the Pelagic Fisheries Research Program to develop a
general framework for modeling protected species. (http://www.soest.hawaii.edu/PFRP/protected_species/maunder.html)
Mark is working on this project in collaboration with
Simon Hoyle. They have developed a model for eastern
spotted dolphin in the EPO and are developing a model
for the Hawaii population of black footed albatross.
Mark is also
collaborating with Jaume Forcada of the
British Antarctic Survey developing models to determine
environmental effects on Antarctic penguin population
dynamics. In previous research he has developed and
implemented models to investigate the tradeoff between
lost commercial squid catch and New Zealand sea lion
recovery under the sea lion population management plan,
and compared it with other management options
|
Stock assessment methods
Mark has carried out several studies into methods to
improve stock assessment. Many of these methods revolve
around the integration of multiple sources of
information into stock assessments and the estimation of
uncertainty. For example, Mark has developed methods to
integrate the standardization of CPUE, tagging data, and
environmental covariates into population dynamics
models. Mark has carried out several studies using
Bayesian analysis for fisheries stock assessment and
conservation modeling. Mark was one of the main
developers of the general stock assessment model
Coleraine (http://www.fish.washington.edu/research/coleraine/),
which integrates several types of data and uses Bayesian
analysis to estimate uncertainty. During 2005 Mark
coordinated the stock assessment methods workshop (http://www.iattc.org/PDFFiles2/Stock-assessment-methods-meeting-noticeNov05ENG.pdf).
Mark is collaborating with scientists at the University
of Oslo on a project developing Integrated statistical
analysis based on likelihood and confidence:
applications to the hare-lynx population cycles and the
status and structure of bowhead whales (http://www.cees.no/?option=com_research&project=9). |
|
. |
. |
CPUE standardisation
Mark has had a particular interest in standardising CPUE
and how indices of abundance developed for CPUE data are
used in stock assessment models. Mark has developed
methods to integrate CPUE standardization into stock
assessment models. In collaboration with Michael Hinton,
Mark has developed a statistical approach to include
habitat information for standardizing longline CPUE
data, extending the work of Hinton and Nakano (IATTC
Bulletin 21: 171-200), and a method to standardize CPUE
data using neural networks. Mark co-authored a review of
CPUE standardization in the journal Fisheries Research [70(2-3):
141-159]
with Andre Punt of the University of Washington. During
2004 Mark coordinated the workshop on developing indices
of abundance from purse-seine catch and effort data (http://www.iattc.org/PDFFiles2/Report_PS_CPUE_meeting_Nov04ENG.pdf).
|
|
. |
. |
|
Reference points
Mark has carried out several
studies of the calculation and use of reference points in
fisheries management. In particular, Mark has focused on
how different gears and the allocation of effort effect
reference points.
He has
also investigated the relationship between the shape
parameter of the Pella-Tomlinson model (IATTC Bulletin 13:
421-458), demographic parameters, and reference points.
During
2003 Mark coordinated a workshop on
reference points for tunas and
billfishes pdf. (22 Kb). |
|
. |
. |
|
AD Model Builder (ADMB)
Mark uses ADMB (http://www.otter-rsch.com/)
for most of his modeling. This is the programming
language used to create A-SCALA. ADMB has automatic
differentiation, which greatly increases the efficiency
of the nonlinear optimization routine, and a MCMC
routine for Bayesian analysis. ADMB has been used to fit
complex nonlinear models with thousands of parameters
simultaneously to multiple types of data and to fit
nonlinear models with fewer parameters to hundreds of
thousands of data points. In addition to many other
projects, Mark used ADMB to produce the general stock
assessment model Coleraine (http://www.fish.washington.edu/research/coleraine/)
and for a general marine mammal population model. ADMB
now has efficient methods to implement nonlinear random
effects models.
In collaboration with John Sibert, Anders
Neilsen, and others, Mark has developed a website and
wiki that provides information on ADMB users,
publications, tutorials, examples, and help (http://admb-project.org/wiki/tiki-index.php?page=ADMB-Wiki).
(also see
ADMBreferences.pdf).
Mark has taught an ADMB course
for several organizations (link to course page). |
|
. |
. |
|
Last
modified:
24 Jul 2007 |
