User’s Guide to ADMB2R: A Set of AD Model Builder Output Routines Compatible with the R Statistics Language

ADMB2R is a collection of AD Model Builder routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 ADMB2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the ADMB2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer ADMB2R to others in the hope that they will find it useful. (PDF contains 30 pages)

User’s Guide to C2R: A Set of C Language Output Routines Compatible with the R Statistics Language

C2R is a collection of C routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 C2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the C2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer C2R to others in the hope that they will find it useful. (PDF contains 27 pages)

User’s Guide to For2R: A Module of Fortran 95 Output Routines Compatible with the R Statistics Language

For2R is a collection of Fortran routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 For2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the For2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer For2R to others in the hope that they will find it useful. (PDF contains 31 pages)

Harmful algal research and response: A human dimensions strategy

Harmful Algal Research and Response: A Human Dimensions Strategy (HARR-HD) justifies and guides a coordinated national commitment to human dimensions research critical to prevent and respond to impacts of harmful algal blooms (HABs). Beyond HABs, it serves as a framework for developing hu-man dimensions research as a cross-cutting priority of ecosystem science supporting coastal and ocean management, including hazard research and mitigation planning. Measuring and promoting commu-nity resilience to hazards require human dimensions research outcomes such as effective risk commu-nication strategies; assessment of community vulnerability; identification of susceptible populations; comprehensive assessment of environmental, sociocultural, and economic impacts; development of effective decision support tools; and improved coordination among agencies and stakeholders. HARR-HD charts a course for human dimensions research to achieve these and other priorities through co-ordinated implementation by the Joint Subcommittee on Ocean Science and Technology (JSOST) In-teragency Working Group on HABs, Hypoxia and Human Health (IWG-4H); national HAB funding programs; national research and response programs; and state research and monitoring programs. (PDF contains 72 pages)

Coral Disease and Health Workshop: Coral Histopathology II

The health and continued existence of coral reef ecosystems are threatened by an increasing array of environmental and anthropogenic impacts. Coral disease is one of the prominent causes of increased mortality among reefs globally, particularly in the Caribbean. Although over 40 different coral diseases and syndromes have been reported worldwide, only a few etiological agents have been confirmed; most pathogens remain unknown and the dynamics of disease transmission, pathogenicity and mortality are not understood. Causal relationships have been documented for only a few of the coral diseases, while new syndromes continue to emerge. Extensive field observations by coral biologists have provided substantial documentation of a plethora of new pathologies, but our understanding, however, has been limited to descriptions of gross lesions with names reflecting these observations (e.g., black band, white band, dark spot). To determine etiology, we must equip coral diseases scientists with basic biomedical knowledge and specialized training in areas such as histology, cell biology and pathology. Only through combining descriptive science with mechanistic science and employing the synthesis epizootiology provides will we be able to gain insight into causation and become equipped to handle the pending crisis. One of the critical challenges faced by coral disease researchers is to establish a framework to systematically study coral pathologies drawing from the field of diagnostic medicine and pathology and using generally accepted nomenclature. This process began in April 2004, with a workshop titled Coral Disease and Health Workshop: Developing Diagnostic Criteria co-convened by the Coral Disease and Health Consortium (CDHC), a working group organized under the auspices of the U.S. Coral Reef Task Force, and the International Registry for Coral Pathology (IRCP). The workshop was hosted by the U.S. Geological Survey, National Wildlife Health Center (NWHC) in Madison, Wisconsin and was focused on gross morphology and disease signs observed in the field. A resounding recommendation from the histopathologists participating in the workshop was the urgent need to develop diagnostic criteria that are suitable to move from gross observations to morphological diagnoses based on evaluation of microscopic anatomy. (PDF contains 92 pages)

International Workshop for Management and Trade of Caiman yacare, Gainsville, FL, 3-5 October 2002

A workshop was held 3-5 October 2002 in Gainesville, Florida, USA to discuss management, conservation and trade in Caiman yacare. Twenty five official participants represented the four yacare range states (Argentina, Bolivia, Brazil, Paraguay), Venezuela, USA, the meeting sponsors (US Fish and Wildlife Service, CITES Secretariat, Louisiana Fur and Alligator Council), TRAFFIC Sur America and Crocodile Specialist Group. A series of country reports detailing yacare management in the four range states were distributed in Spanish and English prior to the meeting and presentations on these and on general principles of crocodilian harvest, conservation and management provided the basis for the discussions. Three working groups considered: • Requirements and field techniques for field data collection. • Requirements and techniques for regulation of harvest. • Requirements and processes for regulation of trade and export. Written reports of working groups and a plenary drafting session were finalized during the meeting and distributed, with the country reports, to participants. The workshop drafted a framework for caiman management and regulation that could be used as a template and adapted for use in each range state. The meeting agreed to convene an ad-hoc working group of range state representatives to continue discussions on the harmonization of caiman management into the future.

Parasitology and pathology of marine organisms of the world ocean

The Symposium in which the communications, as they were called during the meeting, comprising this volume were presented was held at the Zoological Institute of the Academy of Sciences of the U.S.S.R. in Leningrad during 13 to 16 October 1981. Conducted as part of the cooperative program of the U.S.A.-U.S.S.R. Working Group on Biological Productivity and Biochemistry of the World Ocean, the Leningrad meeting was sponsored by the Academy of Sciences of the U.S.S.R. (the Zoological Institute) and the Ministry of Fisheries of the U.S.S.R. (The Scientific Council on Fish Diseases of the Ichthyological Commission). It was an extremely interesting and successful Symposium, offering all participants the opportunity to describe the results of their studies and reviews during the course of the formal presentations and direct interchange between scientists during breaks in the program and the organized and casual social activities. The facilities provided by the Zoological Institute were quite adequate and the assistance offered by its Director, O. A. Scarlato and his staff in organization,logistics, and translation was excellent. Several of our Soviet colleagues presided over the proceedings, as did I. All were businesslike and efficient, yet graceful and accommodating. To O. N. Bauer Jell the brunt of programmatic detail and follow-up. He bore his burdens well and, with Director Scarlato and his staff, including A. V. Gussev and others of the professional and technical staffs of the Zoological Institute, helped make our stay pleasant and the Symposium productive. These organizations and individuals deserve much credit and praise as well as the thanks of their American and British colleagues. (PDF file contains 141 pages.)

Fischereiökonomie im Institut für Seefischerei - Überlegungen für zukünftige Forschungsaktivitäten

With the assignment of the head of the fisheries economics working group at the Institute of Sea Fisheries three from four envisioned positions are now filled. Responsibilities will range from data collection and processing to bio-economic modeling, value adding of the fishing sector, and the assessment of economic consequences of climate change. This also includes general advisory responsibilities on the national and international level.

2005: Rekord-Anlandungen an Nordseegarnelen (Crangon crangon L.) in Europa

Brown shrimp (C. crangon) landings are an important factor and ranked third in landings value of North Sea Fisheries. Landings data are gathered by country and kept separately. However, the Working Group on Crangon Fisheries and Life History (WGCRAN) of the International Council for the Exploration of the Sea (ICES) compiles statistical as well as biological data on brown shrimp. This group has met in Ijmuiden end of May 2006 and found new record landings in 2005 for all three major producers: Germany, The Netherlands and Denmark, summing up with The United Kingdom, Belgium and France to more than 38 000 tonnes of con-sumption shrimp, the highest landings ever recorded.

Die Fischerei im Nordostatlantik im Jahre 2004

Since 1990 North-east Atlantic fish species – arctic cod, saithe, haddock, redfish and Greenland halibut – have been investigated by on-board observers on the German commercial trawler FMS Kiel. These investigations are part of the national data collection regulation established by the European Union in recent years. Collected data are basic data for the scientific assessment of these important fish stocks of the European fisheries. The results of the observed cruises are used by the Arctic Fisheries Working Group of the International Council for the Exploration of the Seas (ICES). Biological investigations were carried out in Norwegian waters and the Barents Sea (ICES Divisions IIa and IIb) on board FMS Kiel in January to March and in August/September 2004. This report presents results of these cruises and an overview about the general fishery situation in 2004.

Bestandskundliche Untersuchungen an wirtschaftlich wichtigen Grundfischbeständen im Nordost-Atlantik

For many years the assessments of the commercially most important demersal fish stocks of cod, haddock, saithe, redfish and Greenland halibut have annually been carried out by the "Arctic Fisheries Working Group" of ICES. The most important results of the actual assessment are given in this report. It shows that the gadoid stocks of cod, haddock and saithe are in good and stable conditions and that the stocks are harvested within safe biological limits. The stocks of redfish and Greenland halibut are still at a low level and outside safe biological limits. Greenland halibut shows a slightly positive trend in spawning stock biomass, several year-classes and recruitment.

Fischereisituation, Probennahme und Zustand der Nutzfischbestände im Nordostatlantik im Jahre 2002

NE-arctic cod, saithe, haddock, redfish and Greenland halibut are important fish stocks of the European fisheries. In many European countries national data sampling projects on commercial fisheries have been established in recent years. Since 1990 German investigations in the NE-Atlantic have been mainly carried out on the commercial trawler FMS KIEL. The results of these sea samplings are used as German basic data for stock assessments of the “Arctic Fisheries Working Group” of the International Council for the Exploration of the Seas (ICES). Biological investigations were carried out in Norwegian waters, the Svalbard area and the Barents Sea (ICES Divisions I, IIa and IIb) on board FMS KIEL in March and October/November 2002. This report presents results of these cruises and an overview over the general fishery situation in 2002. Finally, results and recommendations on the scientific stock assessments of cod, saithe, haddock, redfishand Greenland halibut are reported.

Die Fangmengen an Nordseegarnelen und fischereilicher Aufwand im europäischen Vergleich - Langzeitserien und saisonale Übersicht

Among other tasks the “Working Group on Crangon Fisheries and Life Cycle” of the “International Council for the Exploration of the Sea” collects data on landings and effort in the North Sea brown shrimp fisheries by country. Landings per unit effort data are calculated and all are compared on basis of long-term series as well as on seasonal basis. The development for each country is described and compared for the year 2001 to the ten-year average from 1992 to 2001 were possible, as some data are missing especially for the Netherlands. While the Dutch and British fleets increased their landings substantially in 2001 compared to the previous years, Danish,German and Belgian fishermen had reduced landings. There are regional differences in fishing pattern between the countries, especially Denmark versus the rest of Europe. Effort measures remain incomparable between the countries, and fluctuations in landings per unit effort data seem to be in a normal biological range, giving no reason for concern at present for the situation of brown shrimp stocks in the North Sea. An improvement of the data basis is required and possibly achievable by the EU logbook system being in force for brown shrimp fisheries as well.

Die nordostarktische Fischerei im Jahre 2003

Seasampling of the important northeast Arctic fish stocks cod, saithe, haddock, redfish and Greenland halibut was continued in 2003. The sampling is part of the European data sampling directive on commercial fisheries established in recent years. This directive is relevant for European waters as well as for other areas where quotas have been assigned for European community member states. Furthermore, the results of these samplings are used as German basic data for stock assessments of the “Arctic Fisheries Working Group” of the International Council for the Exploration of the Seas (ICES). This report presents results of biological investigations which were carried out in ICES divisions IIa and IIb on board FMS “KIEL” in January/February and July/August 2003. The last section summarizes results and recommendations on the scientific assessment of the northeast Arctic fish stocks.

Die europäischen Krabbenanlandungen der letzten Jahre: Deutschland Nr. 1

Fishery on brown shrimp has developed towards one of the most important fisheries in the North Sea area in economic terms. Statistical data on European wide landings have been gathered by a working group of the International Council for the Exploration of the Sea. They show relatively stable shares of approximately 50% for Germany, 38% for the Netherlands and 8% for Denmark. Further production originates from Great Britain, France and Belgium. The new log-book regulation of the EU will give similar data improved by better information on fishing areas and fishing effort.