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)

Oyster spat set on natural clutch in the Maryland portion of the Chesapeake Bay (1939 - 1975)

Basically this report is an attempt to document trends in oyster recruitment since 1939 and to relate those trends to the actual oyster harvest throughout the Maryland portion of the Chesapeake Bay. It is also hoped that the data as well as the charts compiled in this report will serve as a reference to aid in future studies on Chesapeake Bay oysters. A few if the major biological factors that affect the natural reproduction of the oyster and environmental degradations that may possibly affect oyster reproduction or harvest in the Chesapeake Bay are also briefly discussed. (PDF contains 32 pages)

Monitoring the trophic status of reservoirs

The current situation of regional, rather' than national, problems of eutrophication in standing waters has been widely aired in recent reports. A reliable, quantitative data base is a prerequisite to future trend monitoring, a concensus view of those reports. The objective of this report is to establish requirements, methodology and a minimal data set for nutrient and algae status in water supply reservoirs in England which may be used as a protocol for future trend monitoring.A pilot study has been carried out to assess the relative merits of different sampling strategies, the choice of which has major implications for the cost of sample collection. This short report suggests that consider the possibility of designating a few sites as ”baseline sites” at which detailed changes in trophic status as monitored by the more labour-intensive parameters would be collected on a regular, long term basis to help in the interpretation of the low cost survey results.

Effective herding of flatfish by cables with minimal seafloor contact

Otter trawls are very effective at capturing flatfish, but they can affect the seaf loor ecosystems where they are used. Alaska f latf ish trawlers have very long cables (called sweeps) between doors and net to herd fish into the path of the trawl. These sweeps, which ride on and can disturb the seaf loor, account for most of the area affected by these trawls and hence a large proportion of the potential for damage to seaf loor organisms. We examined modifications to otter trawls, such that disk clusters were installed at 9-m intervals to raise trawl sweeps small distances above the seafloor, greatly reducing the area of direct seafloor contact. A critical consideration was whether flatfish would still be herded effectively by these sweeps. We compared conventional and modified sweeps using a twin trawl system and analyzed the volume and composition of the resulting catches. We tested sweeps raised 5, 7.5, and 10 cm and observed no significant losses of flatfish catch until sweeps were raised 10 cm, and those losses were relatively small (5–10%). No size composition changes were detected in the flatfish catches. Alaska pollock (Theragra chalcogramma) were captured at higher rates with two versions of the modified sweeps. Sonar observations of the sweeps in operation and the seaf loor after passage confirmed that the area of direct seafloor contact was greatly reduced by the modified sweep

Spatial and temporal patterns in the bycatch of seabirds in the Argentinian longline fishery

Longline fisheries have grown throughout the world’s oceans for more than 40 years. This type of fisheries has captured high-quality fish (mature individuals rather than unwanted juveniles), has had minimal destructive effects on bottom habitats, and has produced a low bycatch of nontargeted fish (Brothers et al., 1999). Seabirds, however, are hooked accidentally when they swallow or are snagged on the baited hooks set by commercial longline crews (Brothers, 1991; Barnes et al., 1997; Tasker et al., 2000; Belda and Sanchez 2001; Jahncke et al., 2001

Ex-ante assessment of integrated aquaculture-agriculture adoption and impact in Southern Malawi

There are increasing requirements for impact assessment by development partners in order to increase the accountability and effectiveness of research and development projects. Impact assessment research has been dominated by conventional economic methods. This context challenges agricultural research organizations to develop and apply alternative impact assessment methods incorporating economic, social, and environmental impact components. In this study, we use the Tradeoff Analysis for Multi-Dimensional Impact Assessment (TOA-MD) model to evaluate the impact of integrated aquaculture-agriculture (IAA) adoption in Malawi. The study demonstrated that with a minimal data set, the TOA-MD model can be applied to predict and assess the adoption rates of new technologies and practices as well as their economic and non-economic impacts.

Diet of the minimal armhook squid (Berryteuthis anonychus) (Cephalopoda: Gonatidae) in the northeast Pacific during spring

The stomach contents of the minimal armhook squid (Berryteuthis anonychus) were examined for 338 specimens captured in the northeast Pacific during May 1999. The specimens were collected at seven stations between 145−165°W and 39−49°N and ranged in mantle length from 10.3 to 102.2 mm. Their diet comprised seven major prey groups (copepods, chaetognaths, amphipods, euphausiids, ostracods, unidentified fish, and unidentified gelatinous prey) and was dominated by copepods and chaetognaths. Copepod prey comprised four genera, and 86% by number of the copepods were from the genus Neocalanus. Neocalanus cristatus was the most abundant prey taxa, composing 50% by mass and 35% by number of the total diet. Parasagitta elegans (Chaetognatha) occurred in more stomachs (47%) than any other prey taxon. Amphipods occurred in 19% of the stomachs but composed only 5% by number and 3% by mass of the total prey consumed. The four remaining prey groups (euphausiids, ostracods, unidentified fish, and unidentified gelatinous prey) together composed <2% by mass and <1% by number of the diet. There was no major change in the diet through the size range of squid examined and no evidence of cannibalism or predation on other cephalopod species.

Column set gill net fishing in Gobindsagar reservoir

Previous authors observed the influence of temperature variations in movement of fishes and noticed better catches in bottom set nets during summer in Tungabhadra reservoir. The present account reports on similar observations in Gobindsagar reservoir.

A pilot scale set up for the manufacture of fish hydrolysate

This paper describes a set up for a pilot plant with a capacity of 50 kg raw material per batch for the production of fish hydrolysate by enzymatic hydrolysis. Process flow sheet and complete specifications and functions of individual equipment have been described. Multifunctional equipment designed for this pilot plant set up has reduced the number of equipment considerably.

Biology and farming of the green mussel Mytilus smaragdinus

Biological investigations were carried out in Sapian Bay, Capiz from November 1975 to December 1976 with samplings conducted fortnightly. Histological studies on the gonad reveal a high percentage of ripe and spent females during the month of April and May, and ripe to near ripe during November to December. However, larval counts were highest on February 25, 1976 with 253 mytilid larvae per haul compared to 0-79 per haul during all other months. The high larval count was followed by the highest spat settlement during the next sampling period two weeks later, with the spat collector set in the water during the February 25 sampling. The four materials tested, blue polypropylene fiber rope, black polypropylene fiber, and coir rope, all had their highest spat counts during this period with an average of 471 spats per standard 10 cm rope piece. The range during the other time periods is 2-283 spats. Of the 4 materials tested, the black fibrillated polypropylene film had the highest larval counts in 15 out of a total of 25 sampling periods. The blue rope was the poorest spat collector. Coconut husk was tested later on and it proved to have a very high catchability, with spats completely enveloping the husk surface. Growth monitored from one cohort in Sapian Bay averaged 10 mm per month. 50-60 mm is considered marketable size. Trial growth experiments with transplanted mussels were also conducted at Igang Bay in Guimaras Island, Makato River in Aklan, and a milkfish pond in Leganes, Iloilo. Survival in Igang was less than 50% after the second week, and the condition of the surviving mussels can be described only as 'watery' with the mantle completely transparent. Mortality was minimal in Makato but the growth rate was only 30% that of Sapian Bay. The pond experiments were terminated due to severe crab predation.

Biology of the penaeid shrimp populations exploited by Estuarine Set Bagnet

Results of analysis of part of the data collected during October, 1989 to December, 1990 are given on the biology and catch assessment studies on the Estuarine Set Bagnet (ESBN) from six sampling stations covering the entire coast line of Bangladesh. Length frequency analysis of seven most commonly occurring penaeid shrimp species have been done with complete ELEFAN software package. The result of exploitation patterns indicate that all penaeids except P. stylifera are being over exploited on their way back to the Sea from the nursery ground. This appeared to be the instances of serious growth over fishing. These species are exploited at a size much lower than the length at first maturity, which strongly suggests a complete withdrawal of the bagnet fishery from the coast of Bangladesh.