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)

Information and knowledge sharing

The Guidelines provide a special focus on information and knowledge sharing and its current and potential role in supporting implementation of the Code of Conduct for Responsible Fisheries. They expand on relevant principles and standards set forth in the Code and make practical suggestions about ways to ensure that this role can be enhanced. The issues involved in the flow of information between different stakeholder groups include topics as diverse as information policy frameworks and information and communication technology infrastructure, hence coverage is introductory. Some of the constraints involved in the cycle from the creation, production, dissemination and availability of information and knowledge to its effective use and sharing by the present generation as well as its preservation for the future are presented. The special circumstances and requirements of stakeholders in developing countries are recognized in accordance with Article 5 of the Code. A separate chapter on small-scale fisheries and aquaculture looks in more detail at the special situation and information needs of the sub-sector. The Guidelines aim to foster a better understanding of the issues involved to ensure that stakeholders obtain the essential information that they need and that they make available their own information and knowledge for the public good. (PDF contains 115 pages)

IBM PC Data Acquisition and Processing Software Evaluation

Commercially available software packages for IBM PC-compatibles are evaluated to use for data acquisition and processing work. Moss Landing Marine Laboratories (MLML) acquired computers since 1978 to use on shipboard data acquisition (Le. CTD, radiometric, etc.) and data processing. First Hewlett-Packard desktops were used then a transition to the DEC VAXstations, with software developed mostly by the author and others at MLML (Broenkow and Reaves, 1993; Feinholz and Broenkow, 1993; Broenkow et al, 1993). IBM PC were at first very slow and limited in available software, so they were not used in the early days. Improved technology such as higher speed microprocessors and a wide range of commercially available software made use of PC more reasonable today. MLML is making a transition towards using the PC for data acquisition and processing. Advantages are portability and available outside support.

Creation of temporary ponds for amphibians in northern and central Europe

More than 4000 ponds have been created or restored in Denmark since 1985 as part of a large-scale pond-digging programme to protect endangered amphibians in particular and pond flora and fauna in general. Most ponds are created on private land with public financing. The programme was triggered by, among other factors, a drastic decline in amphibian populations in Denmark between 1940 and 1980. However, in recent years there has been an increased awareness in Denmark that temporary ponds are important for the conservation of some of the most rare amphibian species, such as fire-bellied toad Bombina bombina, natterjack toad Bufo calamita and green toad Bufo viridis. Other rare species such as moor frog Rana arvalis and European tree frog Hyla arborea also benefit from temporary ponds. The last 15 years of work on the conservation of endangered species and their habitats has resulted in a last-minute rescue and a subsequent growth in the size of most Danish populations of fire-bellied toad and green toad; some populations of the relatively more common natterjack toad have also increased. The creation of temporary ponds plays an important role in the success of these three species. The creation of ponds to help restore viable populations of the most rare amphibians has not been easy. To study the conditions that may need to be created, Danish herpetologists searched for areas with temporary ponds that had good water quality, natural hydrological conditions and a management regime influenced by traditional agricultural methods. The paper gives an overview of pond creation and restoration projects in Denmark and Poland and their significance for amphibian diversity.

A photographic record of a pre- and post-lake creation event from World War II at Valley, Isle of Anglesey, UK

The article compares a recent aerial photograph of the lowlands of the Isle of Anglesey area with a German surveillance photograph from 1941. The authors aim to infer the environmental changes made to this sand dune and lake system as a direct consequence of constructing the airfield. Part of Tywyn Trewan, the extensive sand dune system, was completely destroyed in order to create runways and the technical and domestic accommodation to house a strategic airfield. As part of the dredging, six new water bodies with a combined surface area of approximately 6 ha were created.

River Wyre salmon and sea trout spawning habitat restoration / creation project. Final report April 1995

Adult salmon and sea trout rod catches in the River Wyre have been subject to considerable variability over the years. Annual rod catches ranging from 6 to 401 have been reported since records began in 1905. It has long been suspected that the physical nature of the catchment, combined with anthropogenic influences, has resulted in a deleterious effect on the Wyre fishery. Acidification problems in the head water streams (Marshaw Wyre and Tarnbrook Wyre) have been reported and are thought to threaten salmon juvenile survival. The construction of Abbeystead Reservoir and an increased tendency towards rapidly rising water levels during storms (flashiness) 1 are thought to have a significant impact on spawning gravel quality and quantity, both of which are thought to be deteriorating. As part of an overall desire to maintain and improve the migratory salmonid population in the River Wyre, this project has been commissioned to investigate remedial action which may improve and enhance spawning success, leading to an eventual improvement in the status of adult stocks. The primary objective is to establish whether the quantity and/or quality of available spawning gravels are limiting migratory salmonid productivity. The investigations undertaken confirm the general observation that useable spawning gravels appear to be in short supply in the River Wyre, and may be the limiting factor influencing returning adult stock.

River Wyre salmon and sea trout spawning habitat restoration / creation project. Gravel enhancement schemes.

As part of an overall desire to maintain and improve the migratory salmonid population in the River Wyre, a project was commissioned to investigate remedial action which may improve and enhance spawning success and lead to an eventual improvement in the status of adult stocks. The report, titled "River Wyre Salmon and Sea Trout Spawning Habitat Restoration/Creation Project", concluded that usable spawning gravels appeared to be in short supply in the River Wyre catchment and may be the limiting factor influencing the returning adult stock, as juvenile nursery habitat was not found to be limiting. This report looks at gravel enhancement schemes to improve River Wyre salmon and sea trout spawning habitat restoration. It examines methods for gravel enhancement schemes: mechanical cleaning and construction of gravel addition structures. Includes sites figures of sites identified for enhancement.

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm.

The ECOPATH II software

Problems involved in the development of ecosystem models are discussed, considering in particular the use of the ECOPATH II software and the approach used at ICLARM in the project Global comparisons of trophic aquatic ecosystem models designed to support modelling efforts of research groups throughout the world.

ICLARM software projects: back to the future

The different computer softwares developed by the International Center for Living Aquatic Resources (ICLARM) and its functions and uses in fisheries science are presented.

A computer software package for assessing and managing risks posed by experiments with genetically modified fish and shellfish

Assessment and management of risk is needed for sustainable use of genetically modified aquatic organisms (aquatic GMOs). A computer software package for safely conducting research with genetically modified fish and shellfish is described. By answering a series of questions about the organism and the accessible aquatic ecosystem, a researcher or oversight authority can either identify specific risks or conclude that there is a specific reason for safety of the experiment. Risk assessment protocols with examples involving transgenic coho salmon, triploid grass carp and hybrid tilapia are described. In case a specific risk is identified, the user is led to consider risk management measures, involving culture methods, facilities design and operations management, to minimize the risk. Key features of the software are its user-friendly organization; easy access to explanatory text, literature citations and glossary; and automated completion of a worksheet. Documented completion of the Performance Standards can facilitate approval of a well designed experiment by oversight authorities.