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)

Ecosystem exploitation, sustainability and biodiversity: Are they compatible?

This articles offers a basis for describing sustainability and then seeks to place this concept on an energetic basis by reference to recent advances in the understanding of patterns and processes in (mainly pelagic) fresh waters. Finally, by relating these to terrestrial ecosystems, it is shown how their sustainability may be attained through encouraging healthy fresh waters. Features of population succession are taken from observations on phytoplankton ecology.

Compatibility of Glyphosate with Galerucella calmariensis; a Biological Control Agent for Purple Loosestrife (Lythrum salicaria)

By integrating Galerucella calmariensis with glyphosate there is potential to achieve both immediate and sustained control of purple loosestrife (Lythrum salicaria). The objective of this study was to determine the compatibility of glyphosate on the oviposition and survival of adult G. Calmariensis and on the ability of G. calmariensis third instar larvae to pupate to teneral adults. Our results revealed glyphosate (formulated as Roundup) at a concentration of 2% (2.43L/acre) and 4% solution (4.86 L/acre) had no impact on the ability of G. calmariensis third instar larvae to pupate to new generation adults. To examine the effect of a 2% solution of glyphosate on adult G. calmariensis oviposition and survival, adults were randomly divided between a direct contact group (adults sprayed directly), an indirect contact group (host plants with adults were sprayed), and a control group. Our results revealed that glyphosate does not impact G. calmariensis oviposition or adult survival. The results of this study indicate that G. calmariensis is compatible with glyphosate indicating that further field studies examining integrated control strategies for purple loosestrife are warranted.

Begrenzung des Fischereiaufwandes oder Erhöhung der Mindestmaschenöffnung – Ein Vergleich der Alternativen bei der Dorschfischerei in der Ostsee

The basis for a long-term profitable fishery is a precautionary and environment-compatible use of fish stocks. The fishery management presently models the exploitation through the parameters of fishing mortality and the age at first capture. These two parameters are translated into the technical measures of fishing effort and mesh openings and quotas, which are then used in practice for controlling the fishery. Stock protection can be achieved by reducing the fishing effort, by assigning smaller quotas, by reducing the number of days at sea, or by increasing the mesh opening. The respective protection measures have different effects on the development of the stocks but also on the revenue obtained by the fishery. These alternatives have been examined taking as an example the cod stock in the western Baltic. The optimization goal was the maximization of profit observing at the same time the prerequisites for stock protection according to the precaution approach. For these calculations the same models and data have been used as are beeing used in the stock management of the ACFM of ICES. The response of altered technical measures to the recruitment of cod stock was considered, and a proposal to overcome overfishing of cod in the western Baltic Sea was derived.

Linefish resources annual report for the year 2000. Part 1: fisheries assessment

This work reflects the activities of line and trap fishing in Southern Mozambique in 2000. The catch in line fishing has been estimated at 441 mt, according to the DNAP records. The same sources indicated that 1767 days were spent at sea and the estimated catch rate was 250 Kg per boaticlay. Most of the line fishing effort shifted away from Maputo and moved to Inhambane region. The monthly analysis of fishing vessels, stricter controls over catch and effort data submission, development of long-term research programme and the continuation of the on board sampling to improve the data collection are the recommendation for line fishing. The catch of trap vessels increases from 30mt in 1997 to 172 mt in 2000, during which the total number of traps increased from 25 to 300. During this time the number of fishing days has remained relatively constant, as well the soak time. These data sets are thus not compatible with each other, reflecting an increase in daily catch from 243 Kg to 791 kg. The species composition is mainly dominated by P. coeruleopunctatus, C. puniceus, C. nufar and E. andersoni.

Salmon stocking by the Lancashire River Authority: investigations into the requirements and methods best suited to the area

All species of fish are able to propagate and maintain their numbers provided that no adverse influence occurs to change the compatible environment, the salmon is no exception. Propagation of fish by artificial means has long been a subject of discussion amongst fishery workers and views have been expressed (both favourable and unfavourable) on the merits of the various methods employed. In an attempt to discover whether artificial propagation was necessary and also to find the best methods of propagation to adopt in the various rivers, a phased programme of investigation into natural spawning efficiency and the results obtained by various methods of artificial propagation was started in the Lancashire River Board area during 1957. The object being to seek information on: (1) The survival of ova from natural spawnings to the eyed and alevin stages. (2) The population density of feeding fry (from natural spawnings) at various intervals of development. (3) The viability of green ova and eyed ova- when planted artificially. (4a) The survival to 0+ parr from implants of eyed ova unfed fry and fed fry. (4b) Populations per unit area of 0+ parr from various planting densities of eyed ova, unfed fry and fed fry. Sampling stations were selected on the Rivers Ribble, Lune and Wyre watersheds for the purpose of marking and examination of natural salmon redds.

An ecological characterization of the Stellwagen Bank National Marine Sanctuary Region: oceanographic, biogeographic, and contaminants assessment

The mission of NOAA’s National Marine Sanctuary Program (NMSP) is to serve as the trustee for a system of marine protected areas, to conserve, protect, and enhance their biodiversity, ecological integrity, and cultural legacy while facilitating compatible uses. Since 1972, thirteen National Marine Sanctuaries, representing a wide variety of ocean environments, have been established, each with management goals tuned to their unique diversity. Extending from Cape Ann to Cape Cod across the mouth of Massachusetts Bay, Stellwagen Bank National Marine Sanctuary (NMS) encompasses 2,181 square kilometers of highly productive, diverse, and culturally unique Federal waters. As a result of its varied seafloor topography, oceanographic conditions, and high primary productivity, Stellwagen Bank NMS is utilized by diverse assemblages of seabirds, marine mammals, invertebrates, and fish species, as well as containing a number of maritime heritage resources. Furthermore, it is a region of cultural significance, highlighted by the recent discovery of several historic shipwrecks. Officially designated in 1992, Stellwagen Bank became the Nation’s twelfth National Marine Sanctuary in order to protect these and other unique biological, geological, oceanographic, and cultural features of the region. The Stellwagen Bank NMS is in the midst of its first management plan review since designation. The management plan review process, required by law, is designed to evaluate, enhance, and guide the development of future research efforts, education and outreach, and the management approaches used by Sanctuaries. Given the ecological and physical complexity of Stellwagen Bank NMS, burgeoning anthropogenic impacts to the region, and competing human and biological uses, the review process was challenged to assimilate and analyze the wealth of existing scientific knowledge in a framework which could enhance management decision-making. Unquestionably, the Gulf of Maine, Massachusetts Bay, and Stellwagen Bank-proper are extremely well studied systems, and in many regards, the scientific information available greatly exceeds that which is available for other Sanctuaries. However, the propensity of scientific information reinforces the need to utilize a comprehensive analytical approach to synthesize and explore linkages between disparate information on physical, biological, and chemical processes, while identifying topics needing further study. Given this requirement, a partnership was established between NOAA’s National Marine Sanctuary Program (NMSP) and the National Centers for Coastal Ocean Science (NCCOS) so as to leverage existing NOAA technical expertise to assist the Sanctuary in developing additional ecological assessment products which would benefit the management plan review process.

Marine cage culture and the environment: twenty-first century science informing a sustainable industry

Technological innovation has made it possible to grow marine finfish in the coastal and open ocean. Along with this opportunity comes environmental risk. As a federal agency charged with stewardship of the nation’s marine resources, the National Oceanic and Atmospheric Administration (NOAA) requires tools to evaluate the benefits and risks that aquaculture poses in the marine environment, to implement policies and regulations which safeguard our marine and coastal ecosystems, and to inform production designs and operational procedures compatible with marine stewardship. There is an opportunity to apply the best available science and globally proven best management practices to regulate and guide a sustainable United States (U.S.) marine finfish farming aquaculture industry. There are strong economic incentives to develop this industry, and doing so in an environmentally responsible way is possible if stakeholders, the public and regulatory agencies have a clear understanding of the relative risks to the environment and the feasible solutions to minimize, manage or eliminate those risks. This report spans many of the environmental challenges that marine finfish aquaculture faces. We believe that it will serve as a useful tool to those interested in and responsible for the industry and safeguarding the health, productivity and resilience of our marine ecosystems. This report aims to provide a comprehensive review of some predominant environmental risks that marine fish cage culture aquaculture, as it is currently conducted, poses in the marine environment and designs and practices now in use to address these environmental risks in the U.S. and elsewhere. Today’s finfish aquaculture industry has learned, adapted and improved to lessen or eliminate impacts to the marine habitats in which it operates. What progress has been made? What has been learned? How have practices changed and what are the results in terms of water quality, benthic, and other environmental effects? To answer these questions we conducted a critical review of the large body of scientific work published since 2000 on the environmental impacts of marine finfish aquaculture around the world. Our report includes results, findings and recommendations from over 420 papers, primarily from peer-reviewed professional journals. This report provides a broad overview of the twenty-first century marine finfish aquaculture industry, with a targeted focus on potential impacts to water quality, sediment chemistry, benthic communities, marine life and sensitive habitats. Other environmental issues including fish health, genetic issues, and feed formulation were beyond the scope of this report and are being addressed in other initiatives and reports. Also absent is detailed information about complex computer simulations that are used to model discharge, assimilation and accumulation of nutrient waste from farms. These tools are instrumental for siting and managing farms, and a comparative analysis of these models is underway by NOAA.

Distribution, biology and behaviour of the giant trevally, Caranx ignobilis- a candidate species for mariculture

Fishery and biology of the giant trevally, Caranx ignobilis exploited along the Tuticorin coast of Tamilnadu were monitored during 2001-2006. Fishery occurred round the year with peak landings during April-August. Spawning and recruitment occur almost round the year with peak during November-December. Young ones are abundant in shallow coastal waters and as grows, they move to deeper waters. Growth parameters, L"' and K are estimated respectively as 143.6 cm and 0.69/year and 'to' as -0.0242 year. Estimates show that they grow fast and attain 73, 108, 126 and 134 cm in total length by first, second, third and fourth year respectively. Their weight increment is also fast and attains 5.5 kg, 16.8 kg, 25.9 kg and 33.7 kg respectively during the period. Stock assessment indicated that the stock at present is over exploited and under heavy fishing pressure. Rearing trial in aquarium tank showed that they are compatible to confined rearing conditions. Based on the distribution and biology of the species, their mariculture potential is discussed.