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)

Uganda and Malawi field pilots of proposed LSMS fisheries module: summary report

While an overwhelming majority of sub-Saharan African countries exhibit serious weaknesses in statistics pertaining to crop and livestock sectors, the deficiencies in terms of nationally representative data on the fishery sector are even more acute. The very little data available on the sector are essentially derived from case studies of selected fisheries, and the limited nationally representative data available are generally derived from a few questions included in the livestock section of household surveys. These do not permit the detailed characterization of the fishery production systems. As a consequence in many countries the decision-makers and planners lack the most basic information about the role and importance of the fisheries sector to their national economy. As part of an initiative called the Living Standards Measurement Study-Integrated Surveys on Agriculture (LSMS-ISA) project, a collaboration was developed between the World Bank and the WorldFish Center to address this situation. This report provides detail on pilot testing of a fisheries module for living standards measurement surveys.

Carmel Lagoon Water Quality and Steelhead Soundings: Fall 2007

ESSP 660 Advanced Watershed Science and Policy is a graduate class taught in the Master of Science in Coastal and Watershed Science & Policy program at California State University Monterey Bay. In 2007, the class was taught in four 4-week modules, each focusing on making a small contribution to a local watershed issue. This report describes the results of one of those 4-week modules – on Carmel Lagoon Water Quality and Ecology. The module was lead instructed by Fred Watson (CSUMB) and Kevan Urquhart (MPWMD). (Document contains 54 pages)

Observations of the biological communities at Bolsa Chica artificial reef

Bolsa Chica Artificial Reef (BCAR) was constructed in November 1986 with 10,400 tons of concrete rubble and eight concrete and steel barges. Prior to any additional augmentation of BCAR, the u.s. Army Corps of Engineers and the California Coastal Commission required the California Department of Fish and Game (CDFG) to survey the bioloqical communities on and around BCAR. In April 1992, qualitative surveys of the biological communities were conducted on one of the eight modules at BCAR and at a nearby sand-only site. One of the modules, Module D, located in 90 feet of water (MLLW), was surveyed for fish, macroinvertebrates, and turf community organisms (small plants and sessile animals). Twelve species of fish were observed, including kelp bass (Paralabrax clathratus) and barred sand bass (P. nebulifer). Eight macroinvertebrate species were observed, rock scallops (Crassedoma giganteum) being the most abundant. The turf community was comprised of thirteen invertebrate taxa, among which erect ectoprocts (Bugula spp.) were the most numerous. Two species of foliose red algae (Rhodymenia pacifica and Anisocladella pacifica) were also observed. The reef has reached an advanced stage of successional development with fish and invertebrate communities diverse and well established. However, due,.to its depth and the turbidity of surrounding waters, this reef is not likely to ever support a diverse algal community. The diversity and abundance of fish and macroinvertebrates were, as to be expected, much lower in the nearby sand-only site. Only two species of fish and seven macroinvertebrate species were observed. Of these, only the sea pen, Stylatula elongata, was common. Overall, when compared to nearby sand-only habitats, Bolsa Chica Artificial Reef appears to contribute substantially to the local biological productivity. In addition, the concrete rubble used in BCAR' s construction appears to be performing as well as the quarry rock used in all of CDFG's experimental reefs. (Document pdf contains 22 pages)

MAPPER, a low-level geographic information system

A Low-Level Geographic Information System (LL-GIS) was developed to provide a simple low-cost mapping program which can be executed in any personal computer, by individuals with different levels of knowledge in computing. MAPPER is an add-on module of FishBase - a global database with key information on the biology of fish - where it creates on-screen maps with information on biodiversity and the occurrence of species. In another application, MAPPER is used to display and analyzed geographical information on the Philippines.

A low-level geographic information system for coastal zone management with applications to Brunei Darussalam: Part III:: simulation and tracking oil spills

B:RUN is a low-level GIS software designed to help formulate options for the management of the coastal zone of Brunei Darussalam. This contribution presents the oil spill simulation module of B:RUN. This simple module, based largely on wind and sea surface current vector parameters, may be helpful in formulating relevant oil spill contingency plans. It can be easily adapted to other areas, as can the B:RUN software itself.

Announcing the release of FishBase 96

FishBase is a computerized encyclopedia of fishes developed at International Center for Living Aquatic Resources Management (ICLARM) with the support of the European Commission and in collaboration with a large number of institutions throughout the world, notably FAO, and available since 1995 as CD-ROM. Major improvements since version 1.2 have now allowed for the release of FishBase 96, whose name indicates the intention to update FishBase annually. Some of the major improvements of FishBase 96 are: (a) 3,000 more species (total 15,000) and 3,000 more pictures (total 9,000); (b) complete marine checklists for 48 countries, and freshwater checklists for 60 countries; (c) a new user module to document local knowledge of fishes; (d) a stand-alone glossary defining 2,500 ichthyological and related terms; (e) new databases on brain weights (from R. Beauchot and colleagues at the University of Paris VII), on ciguatera (from P. Dalzell, South Pacific Commission, Noumea), and on recruitment (from R.A. Myers and colleagues at the Department of Fisheries and Oceans, St. John's); and (f) new graphs to display quantitative data: through time series, pie charts and bivariate plots. As before, FishBase is available free to collaborators, for US$50 as update to registered users of previous versions, and for US$95 for new users.

The EBM-DPSER conceptual model: integrating ecosystem services into the DPSIR framework

There is a pressing need to integrate biophysical and human dimensions science to better inform holistic ecosystem management supporting the transition from single species or single-sector management to multi-sector ecosystem-based management. Ecosystem-based management should focus upon ecosystem services, since they reflect societal goals, values, desires, and benefits. The inclusion of ecosystem services into holistic management strategies improves management by better capturing the diversity of positive and negative human-natural interactions and making explicit the benefits to society. To facilitate this inclusion, we propose a conceptual model that merges the broadly applied Driver, Pressure, State, Impact, and Response (DPSIR) conceptual model with ecosystem services yielding a Driver, Pressure, State, Ecosystem service, and Response (EBM-DPSER) conceptual model. The impact module in traditional DPSIR models focuses attention upon negative anthropomorphic impacts on the ecosystem; by replacing impacts with ecosystem services the EBM-DPSER model incorporates not only negative, but also positive changes in the ecosystem. Responses occur as a result of changes in ecosystem services and include inter alia management actions directed at proactively altering human population or individual behavior and infrastructure to meet societal goals. The EBM-DPSER conceptual model was applied to the Florida Keys and Dry Tortugas marine ecosystem as a case study to illustrate how it can inform management decisions. This case study captures our system-level understanding and results in a more holistic representation of ecosystem and human society interactions, thus improving our ability to identify trade-offs. The EBM-DPSER model should be a useful operational tool for implementing EBM, in that it fully integrates our knowledge of all ecosystem components while focusing management attention upon those aspects of the ecosystem most important to human society and does so within a framework already familiar to resource managers.

Mercury bioaccumulation in pike (Esox lucius) food chain from Anzali Lagoon, Iran

A number of wide-ranging monitoring studies have been performed in order to estimate the degree of mercury (Hg) contamination in freshwater ecosystems. Knowledge regarding contamination of different levels of the food chain is necessary for estimation of total pollutant input fluxes and subsequent partitioning among different phases in the aquatic system. The growing international concern about this environmental data is closely related to the strongly developing ecological risk assessment activities. In addition,freshwater monitoring outputs hold a key position in the estimation of the Hg dose consumed by the human population as it is highly dependent on fish consumption. So monitoring of Hg in the tissue of edible fish is extremely important because of contaminated fish has caused serious neurological damage to new born babies and adults. Mercury tends to accumulate in fish tissue, particularly, in the form of methyl mercury, which is about 10 times more toxic than inorganic mercury. The Anzali lagoon is one of the biggest wetland of Guilan province, which joins to the Caspian sea. Many Chemical and industrial factories plus agricultural runoffs and urban and rural sewages are major polluting sources of the Anzali wetland. Since many of those polluting sources drain their wastes directly or indirectly into the Anzali wetland and their sewages may be polluted with Hg, this study was conducted to find out the bioaccumulation of Hg bioaccumulation in pike (Esox lucius) food chain from Anzali lagoon, Iran. Sampling were carried out from July 2004 to July 2005, in addition 318 speciments of 9 fish species were collected. T-Hg was measured by LECO AMA 254 Advanced Mercury Analyzer (USA) according to ASTM standard No D-6722. Each sample was analyzed 3 times. Accuracy of T-Hg analysis was checked by running three samples of Standard Reference Materials; SRM 1633b, SRM 2711 & Sra 2709. Detection limit was 0.001 mg/kg in dry weight. The Accuracy degree of analyzor equipment with RSD<%0.05 (N=7) was between %95.5 and %105. In overal eigth fish species were distingushed in the gut content of 87 speciments of pike with age 1-5 year and maximum length 550mm. The max. and min. concentration of T-Hg in dorsal muscle of pjke was 0.2ppm in one year and 1.2ppm in five year class. The mean of T-Hg significantly increased with age and length increased (P<0.05).Mercury accumulation pattern in pike was as well as muscle > liver > spleen (P<0.05). THg content in female was higher than male(P<0.05). In contrast the mean of THg concentration in dorsal muscle of eigth fish species as prey was 0.282, 0.261, 0.328, 0.254, 0.256, 0.286, 0.322 and 0.241 ppm for Carassius auratus gibelio, Hemiculter leucisculus, Blicca bjoerkna transcaucasica, Chalcalburnus mossulensis, Rhodeus sericeus amarus, Gambusia holbrooki, Alburnus charusini hohenackeri & Scardinius Erythrophthalmus respectively.Liner regresion indicated that high degree of relationship between age of pike and Uptak/Intake ratio (R2=%99.12) and indicated that the mercury bioaccumulation in the pike dorsal muscle increased with age increased. BFA was >1 and and indicating the mercury biomagnification in the pike food chain. Trophy level of pike in the Anzali lagoon was estimated as well as 3.5 and 4 . It is generally agreed that Hg concentration in carnivorous fish are higher than in noncarnivorous species.