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)

The Effects of Salinity, Temperature, and Food on the Growth and Reproductive Output of Polydora nuchalis Woodick, 1953

Polydora nuchalis Woodwick, 1953 (Polychaeta: Spionidae) is a protandric hermaphrodite commonly inhabiting intertidal mud flats in southern California. The species exhibits lecithotrophic larval development and adelphophagia. Reproduction of P. nuchalis was monitored for a year at four sites: Catalina Harbor, San Gabriel River, Huntington Harbour, and Malibu Lagoon. Females deposited from 11 to 31 egg capsules in their tubes, with up to 230 eggs per capsule. An average of 3% of the eggs developed into larvae: the remaining were nurse eggs serving as food for the developing larvae. Reproductive output was quantified by determining the number and size of larvae and nurse eggs for individual capsules. Significant differences among the four populations were found for all the quantified variables. In addition, two size classes of nurse eggs were found to exist in capsules from all of the sites. Egg capsules were found throughout the year at San Gabriel River, but none were found during the winter months at the remaining three sites. Size/frequency data for juveniles and adults of the Catalina Harbor population indicate an annual cycle of recruitment. The laboratory experiment consisted of a 3 x 3 x 2 £actor1al design with replication testing the effects of temperature, salinity, and food supply on growth and reproduction of P. nuchalis. Increasing temperature resulted in significantly increased survivorship, growth rates, and percentage reproduction. It also produced a significant decrease in the size of the nurse eggs and the volume of food per larva. The number of egg capsules was maximum at the intermediate temperature. Increasing the salinity resulted in significant increases in survivorship and Class I nurse egg size. Increaaing food availability produced a significant increase in the percentage of worms reproducing. The interactive effect of salinity and £ood level produced significant changes in the number of larvae per capsule and the number of nurse eggs per capsule. However, the number of nurse eggs per larva did not differ significantly among the experimental treatment groups. (PDF contains 129 pages)

An examination of fluctuations in the “concentration index” of purse seiners and baitboats in the fishery for tropical tunas in the Eastern Pacific, 1951-1961

ENGLISH: In the eastern Pacific Ocean nearly all of the commercial catches of yellowfin tuna (Thunnus albacares) and skipjack (Katsuwonus pelamis) are taken by two types of vessels, baitboats, which use pole and line in conjunction with live-bait, and purse-seiners. From its inception until very recently (1959), this fishery was dominated by baitboats. This method of fishing has been described by Godsil (1938) and Shimada and Schaefer (1956). From 1951 through 1958 baitboats caught between 66.4 and 90.8 per cent of the yellowfin and between 87.2 and 95.3 per cent of the skipjack landed by the California-based fleet. These vessels fished for tuna throughout the year and covered virtually all of the area from southern California to northern Chile. The purse-seine fishery for tunas developed out of the round-haul net fisheries for California sardines and other species. Scofield (1951) gives a detailed description of the development of gear and fishing methods. Prior to 1959 many of the seiners engaged in other fisheries during the fall and early winter months and consequently most of the fishing effort for tuna occurred in the period February-August. The vessels were quite small, averaging approximately 120 tons carrying capacity (Broadhead and Marshall, 1960), in comparison to the baitboats, of which the most numerous size-class was 201-300 tons. The seiners were naturally more restricted in range than the baitboats and most of their effort was restricted to the northern grounds. During the period 1959-61 most of the large baitboats were converted for purse-seining and the existing seiner fleet was modernized. These developments increased the range of the seiner fleet and resulted in a wider and more nearly even spatial and temporal distribution of effort. By the early part of 1961, the purse-seine fleet approximated the level of the preconversion baitboat fleet in amount of effort applied and area covered. The changes in the purse-seine fishery and the fishing methods employed in the modernized fleet are described by Orange and Broadhead (1959), Broadhead and Marshall (1960), McNeely (1961) and Broadhead (1962). The change in the relative importance of the two gears is illustrated by the decline in the proportion of the total logged tonnage landed by California-based baitboats, in comparison to the proportion landed by seiners. In 1959 baitboats landed 49.5 per cent of the yellowfin and 87.8 per cent of the skipjack. In 1960 these percentages were 22.9 and 74.7 respectively and in 1961 the decline continued to 12.6 per cent of the yellowfin and 30.0 per cent of the skipjack (Schaefer, 1962). In previous Bulletins of this Commission (Griffiths, 1960; Calkins, 1961) the baitboat catch and effort statistics were used to compute two indices of population density and an index of concentration of fishing effort and the fluctuations of these indices were analyzed in some detail. Due to the change in the relative importance of the two gears it is appropriate to extend this investigation to include the purse-seine data. The objectives of this paper are to compute two indices of population density and an index of concentration of fishing effort and to examine the fluctuations in these indices before and after the changes in the fishery. A further objective is to compare the purse-seine indices with those of the baitboats for the same time periods. SPANISH: En el Océano Pacífico Oriental casi todas las capturas comerciales del atún aleta amarilla (Thunnus albacares) y del barrilete (Katsuwonus pelamis) son efectuadas por dos tipos de barcos, los barcos de carnada que emplean la caña y el anzuelo en conjunto con la carnada viva, y los barcos rederos. Desde su comienzo hasta hace poco tiempo (1959), esta pesquería estaba dominada por los barcos de carnada. El método de pesca usado por estos barcos ha sido descrito por Godsil (1938) y por Shimada y Schaefer (1956). De 1951 a 1958, los barcos de carnada pescaron entre el 66.4 y el 90.8 por ciento del atún aleta amarilla y entre el 87.2 y el 95.3 por ciento del barrilete descargados por la flota que tiene su base en California. Estos barcos pescaron atún durante todo el año y cubrieron virtualmente toda el área de California meridional hasta la parte norte de Chile. La pesquería del atún con redes de cerco se originó en las pesquerías de las sardinas de California y otras especies, con redes que se remolcaban circularmente. Scofield (1951) dá una descripción detallada del desarrollo de los métodos y del equipo de pesca. Antes de 1959 muchos de los rederos se dedicaban a otras pesquerías durante los meses del otoño y a principios del invierno y consecuentemente, la mayor parte del esfuerzo depesca para la producción del atún ocurría en el período febrero-agosto. Las embarcaciones eran bastante pequeñas, con un promedio de aproximadamente 120 toneladas de capacidad para el transporte (Broadhead y Marshall, 1960) en comparación con los barcos de carnada, de los cuales la clase de tamaño más numerosa era de 201 a 300 toneladas. Los rederos estaban naturalmente más restringidos en su radio de acción que los barcos de carnada y la mayor parte de su esfuerzo se limitaba a las localidades del norte. Durante el período 1959-61, la mayoría de los grandes barcos de carnada fueron convertidos al sistema de pesca con redes de cerco, y se modernizó la flota existente de los rederos. Estos cambios aumentaron el alcance de la flota de los barcos rederos dando como resultado una distribución más amplia y casi más uniforme del esfuerzo espaciado y temporal. En la primera parte del año 1961, la flota de rederos se aproximó al nivel de la preconversión de la flota de clipers, en la cantidad de esfuerzo aplicado y al área comprendida. Los cambios en la pesquería con red y los métodos de pesca empleados en la flota modernizada, han sido descritos por Orange y Broadhead (1959), Broadl1ead y Marshall (1960), McNeely (1961) y Broadhead (1962). El cambio en la importancia relativa de los dos sistemas de pesca está ilustrado por la declinación en la proporción del tonelaje total registrado, como descargado por los barcos de carnada que tienen su base en California, comparado con la proporción desembarcada por los barcos rederos. En 1959 los clipers descargaron el 49.5 por ciento del atún aleta amarilla y el 87.8 por ciento del barrilete. En 1960 estos porcentajes fueron del 22.9 y 74.7 respectivamente, y en 1961 continuó la reducción hasta el 12.6 por ciento del atún aleta amarilla y el 30.0 por ciento del barrilete (Schaefer, 1962). En Boletines anteriores de la Comisión (Griffiths, 1960; Calkins, 1961) las estadísticas de la pesca y el esfuerzo de los clipers se utilizaron para computar dos índices de la densidad de población y un índice de la concentración del esfuerzo de pesca, y se analizaron algo detalladamente las fluctuaciones de estos índices. Debido al cambio en la importancia relativa de los dos sistemas de pesca, es conveniente extender esta investigación para incluir los datos correspondientes a los barcos rederos. Los objetivos del presente estudio son de computar dos índices de la densidad de población y un índice de la concentración del esfuerzo de pesca, y examinar las fluctuaciones en estos índices, antes y después de los cambios en la pesquería. Otro objetivo es de comparar los índices de los barcos rederos, con aquellos de los clipers en los mismos períodos de tiempo.

Aspects of the fishing industry and an overview of artificial reefs and fish aggregating devices for increasing fisheries output and viability in Nigeria

Aspects of the Nigerian fishing industry are outlined to explain the concept of fishing systems viability which is often influenced by a combination of factors including biological productivity, as well as technical, economic and social factors. The productivity of the aquatic environments can be increased by the construction and installation of artificial reefs and fish aggregating devices. These man-made structures provide shelters, food and breeding grounds for fin fish and shell fish. The habitat enhancement techniques are appropriate, efficient, cheap and simple strategic options for increase in fish production. Recommendations for effective utilization and long term management are outlined.

Estimating input demand and output supply elasticities in gillnet and seine fishing in Guimaras Strait and adjacent waters

This contribution is a summary of the results of the study conducted by the University of the Philippines in the Visayas team from November 1990 to June 1991. The purpose of this research is to estimate demand and output supply elasticities in gillnet and seine fishing in Guimaras Strait (Philippines) and adjacent waters.

Do fluctuations in the somatic growth rate of rock lobster (Jasus lalandii) encompass all size classes? A re-assessment of juvenile growth

Catch rates in the South African rock lobster (Jasus lalandii) fishery declined after 1989 in response to reduced adult somatic growth rates and a consequent reduction in recruitment to the fishable population. Although spatial and temporal trends in adult growth are well described, little is known about how juvenile growth rates have been affected. In our study, growth rates of juvenile rock lobster on Cape Town harbor wall were compared with those recorded at the same site more than 25 years prior to our study, and with those on a nearby natural nursery reef. We found that indices of somatic growth measured during 1996–97 at the harbor wall had declined significantly since 1971–72. Furthermore, growth was slower among juvenile J. lalandii at the harbor wall than those at the natural nursery reef. These results suggest that growth rates of juvenile and adult J. lalandii exhibit similar types of spatiotemporal patterns. Thus, the recent coastwide decline in adult somatic growth rates might also encompass smaller size classes.

Strong, low frequency (decadal) environmental fluctuations during the 20th century in the North Pacific Ocean, on the Washington coast, and in Puget Sound

At decadal period (10-20 years), dynamic linkage was evident between atmospheric low pressure systems over the North Pacific Ocean and circulation in a Pacific Northwest fjord (Puget Sound). As the Aleutian low pressure center shifts, storms arriving from the North Pacific Ocean deposit varying amounts of precipitation in the mountains draining into the estuarine system; in turn, the fluctuating addition of fresh water changes the density distribution near the fjord basin entrance sill, thereby constraining the fjord's vertical velocity structure. This linkage was examined using time series of 21 environmental parameters from 1899 to 1987. Covariation in the time series was evident because of the strong decadal cycles compared with long-term averages, interannual variability, and seasonal cycles.

Semiempirical down-scaling of GCM output to the local scale for temperature, precipitation, and runoff

EXTRACT (SEE PDF FOR FULL ABSTRACT): An empirically derived multiple linear regression model is used to relate a local-scale dependent variable (either temperature, precipitation, or surface runoff) measured at individual gauging stations to six large-scale independent variables (temperature, precipitation, surface runoff, height to the 500-mbar pressure surface, and the zonal and meridional gradient across this surface). ...The area investigated is the western United States. ... The calibration data set is from 1948 through 1988 and includes data from 268 joint temperature and precipitation stations, 152 streamflow stations (which are converted to runoff data), and 24 gridded 500-mbar pressure height nodes.

Fluctuations in species composition of Penaeid prawns in estuaries

During a study of the distribution of penaeid prawns in Sri Lanka waters a difference was noticed in the species composition from one estuary to another. Moreover, a marked monthly fluctuation in the relative abundance of the different penaied species was also observed. This indicated migratory behaviour. In order to study this phenomenon in the different species of prawns, regular samples of prawns were collected from two estuaries on the south-west coast of Sri Lanka, namely at Moratuwa/Panadura and at Negombo. The investigation was spread over a period of three years from 1957-1959.

Input-output relationship and economics of pangas monoculture and carp-pangas polyculture in two districts of Bangladesh

An attempt was made to study the input-output relationships and economics of pangas monoculture and carp-pangas polyculture in Bangladesh. By analyzing the data collected from 50 pangas farms and 55 carp-pangas farms, the study has investigated the production systems of two technologies and the effects of fingerling stocking and applications of feed and fertilizer on fisheries income. The data were collected from the fishermen of Trishal and Bhaluka of Mymensingh district, and Kahaloo and Adamdighee of Bogra district during 2001-02. For pangas monoculture, the stocking density was 31,561 per ha while it was 55,017 per ha in carp-pangas polyculture. Most of the farmers used urea, TSP and lime before stocking. Rice and wheat bran happened to be the most common feed ingredients for both types of culture in general. Other important ingredients used were mustard oil-cakes, rice polish, wheat flour, fish meal, bone meal, soybean meal and poultry litter. In terms of quantities, rice bran and wheat bran dominated the farmers list. Rice and wheat bran together constituted about 60% of all studied feeds. Feed cost constituted 59.13% of total costs for pangas monoculture and 67.44% for carp-pangas polyculture. Per ha productions of pangas and carp-pangas in a single culture cycle were 15,508 kg and 19,745 kg, respectively. Per ha gross profits were estimated to be Tk 310,311 and Tk 464,418 for pangas monoculture and carp-pangas polyculture, respectively. Net profit appeared to be Tk 264,216 per ha for pangas monoculture and Tk 416,509 per ha for carp-pangas polyculture. The BCRs calculated were 1.46 and 1.68 for monoculture and polyculture, respectively. The break-even costs per kg of fish were estimated at Tk 36.93 for pangas and Tk 30.93 for mixed species which was much lower than the prices the producers received. Break-even productions were estimated at 10,702 kg per ha for pangas monoculture and 11,784 kg per ha for carp-pangas polyculture. Fingerling and feed cost, and pond size significantly explained the variation of income from pangas monoculture. These factors have significantly influenced the income from the crop. Functional analysis shows that 1% increase in the feed cost might increase 0.51% of pangas income and 0.41% in carp-pangas income. No other inputs had shown this much of responses to increasing income from a fish.