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)

Frame survey of Kainji Lake, northern Nigeria, 1996

Since 1993, annual frame surveys have been conducted by the Nigerian-German Kainji Lake Fisheries Promotion Project to determine the distribution and number of fishing localities, fishing canoes and fishing gears around Kainji Lake, Nigeria. The total number of fishing localities has increased from 221 in 1993 to 286 in 1996. The fishing localities included 245 permanent fishing villages, 29 permanent fishing camps, 8 temporary fishing camps (with fishermen from Kainji Lake) and 4 temporary fishing camps (with fishermen from outside Kainji Lake area). There was an increase in the total number of fishing entrepreneurs, fishing assistants and fishing canoes over the years. A total number of 5,499 fishing entrepreneurs, 12,449 fishing assistants and 9,278 fishing canoes were recorded during the 1996 frame survey. From 1995 there was a decrease in the number of shoreline fisherfolk and a decrease in the number of transport canoes, the number of engines remained the same. During the 1996 survey, a total number of 18,655 gill nets, 1,560 drift nets, 753 beach seines, 5,548 cast nets, 7,400 longlines and 36,979 traps were recorded. The concentration of the gears (number per km shoreline) was highest in substrata 06 and 08. The total number of gill nets increased from 17,680 in 1995 to 18,655 in 1996. For the remaining 5 gear types a decrease in number was observed. Despite increasing numbers of gears on the lake, of concern is the decline recorded in all the fishing methods of the number of gears owned by individual entrepreneurs. This was most notable in the gill net and longline fisheries. These two fisheries have the lowest daily catch values and coupled with the problem of gear theft on the lake, ownership in future, may be expected to fall further. The number of larger fishing units also declined as did the number of gears new entrants enter the fishery with. The decline is particularly worrying for the beach seine fishery where diversification into other fishing methods would be beneficial in light of the present ban on seines. The group of not active fishing entrepreneurs (those who do not themselves participate in fishing activities) had the highest ownership of gears whilst the new entrants into the fishery had the lowest. There was evidence that these new entrants into the fishery were using cast nets which is worrying given the trend of using smaller mesh size of this gearSince 1993, annual frame surveys have been conducted by the Nigerian-German Kainji Lake Fisheries Promotion Project to determine the distribution and number of fishing localities, fishing canoes and fishing gears around Kainji Lake, Nigeria. The total number of fishing localities has increased from 221 in 1993 to 286 in 1996. The fishing localities included 245 permanent fishing villages, 29 permanent fishing camps, 8 temporary fishing camps (with fishermen from Kainji Lake) and 4 temporary fishing camps (with fishermen from outside Kainji Lake area). There was an increase in the total number of fishing entrepreneurs, fishing assistants and fishing canoes over the years. A total number of 5,499 fishing entrepreneurs, 12,449 fishing assistants and 9,278 fishing canoes were recorded during the 1996 frame survey. From 1995 there was a decrease in the number of shoreline fisherfolk and a decrease in the number of transport canoes, the number of engines remained the same. During the 1996 survey, a total number of 18,655 gill nets, 1,560 drift nets, 753 beach seines, 5,548 cast nets, 7,400 longlines and 36,979 traps were recorded. The concentration of the gears (number per km shoreline) was highest in substrata 06 and 08. The total number of gill nets increased from 17,680 in 1995 to 18,655 in 1996. For the remaining 5 gear types a decrease in number was observed. Despite increasing numbers of gears on the lake, of concern is the decline recorded in all the fishing methods of the number of gears owned by individual entrepreneurs. This was most notable in the gill net and longline fisheries. These two fisheries have the lowest daily catch values and coupled with the problem of gear theft on the lake, ownership in future, may be expected to fall further. The number of larger fishing units also declined as did the number of gears new entrants enter the fishery with. The decline is particularly worrying for the beach seine fishery where diversification into other fishing methods would be beneficial in light of the present ban on seines. The group of not active fishing entrepreneurs (those who do not themselves participate in fishing activities) had the highest ownership of gears whilst the new entrants into the fishery had the lowest. There was evidence that these new entrants into the fishery were using cast nets which is worrying given the trend of using smaller mesh size of this gear. (PDF contains 44 pages)

Diets of and trophic relationships among dominant marine nekton within the northern California Current ecosystem

In this study we analyzed the diets of 26 nekton species collected from two years (2000 and 2002) off Oregon and northern California to describe dominant nekton trophic groups of the northern California Current (NCC) pelagic ecosystem. We also examined interannual variation in the diets of three nekton species. Cluster analysis of predator diets resulted in nekton trophic groups based on the consumption of copepods, euphausiids, brachyuran larvae, larval juvenile fishes, and adult nekton. However, many fish within trophic groups consumed prey from multiple trophic levels—euphausiids being the most widely consumed. Comparison of diets between years showed that most variation occurred with changes in the contribution of euphausiids and brachyuran larvae to nekton diets. The importance of euphausiids and other crustacean prey to nekton indicates that omnivory is an important characteristic of the NCC food web; however it may change during periods of lower or higher upwelling and ecosystem production.

Lobster trap debris in the Florida Keys National Marine Sanctuary: distribution, abundance, density, and patterns of accumulation

The fishery for spiny lobster Panulirus argus in the Florida Keys National Marine Sanctuary is well chronicled, but little information is available on the prevalence of lost or abandoned lobster traps. In 2007, towed-diver surveys were used to identify and count pieces of trap debris and any other marine debris encountered. Trap debris density (debris incidences/ha) in historic trap-use zones and in representative benthic habitats was estimated. Trap debris was not proportionally distributed with fishing effort. Coral habitats had the greatest density of trap debris despite trap fishers’ reported avoidance of coral reefs while fishing. The accumulation of trap debris on coral emphasizes the role of wind in redistributing traps and trap debris in the sanctuary. We estimated that 85,548 ± 23,387 (mean ± SD) ghost traps and 1,056,127 ± 124,919 nonfishing traps or remnants of traps were present in the study area. Given the large numbers of traps in the fishery and the lack of effective measures for managing and controlling the loss of gear, the generation of trap debris will likely continue in proportion to the number of traps deployed in the fishery. Focused removal of submerged trap debris from especially vulnerable habitats such as reefs and hardbottom, where trap debris density is high, would mitigate key habitat issues but would not address ghost fishing or the cost of lost gear.

Fecundity of the snow-trout, Schizothorax plagiostomus (Heckel) from Garhwal Himalaya

Absolute fecundity of Schizothorax plagiostomus varied from 3474 in a fish measuring 345 mm (T.L.) and weighing 315 g to 13916 in a fish measuring 540 mm (T.L.) and weighing 1370 g. The weight of the fish ovaries accounted for 7.02 to 17.78% of the total weight of the fish. The average number of eggs per kg weight of fish and per gram of ovary weight was found to be 10820 and 81 respectively. The fecundity per kg of body weight was found to be 11539. The relationships between fecundity and other parameters (fish length/fish weight/ovary weight/ovary volume/ovary length) and fish length-ovary weight and fish weight-ovary weight were also determined.

Polyculture of freshwater prawn, Macrobrachium rosenbergii, de Man with carps: effects of prawn stocking density

Effects of three stocking densities, viz., 35, 50 and 65/decimal (1 decimal = 40.48 m2) of juvenile freshwater prawn (Macrobrachium rosenbergii) on prawn and fish production were tested in a polycuture system with silver carp (Hypophthalmichthys molitrix), catla (Catla catla), Grass carp (Ctenophmyngodon idella) and silver barb (Barbodes gonionotus). The fish stocking density was 19/decimal with the species combination of silver carp-10, catlac-6, grass carp-1 and silver barb-2. In a 8-month culture period, the prawn yield 423 ± 144 kg/ha was significantly lower (P< 0.5) with the prawn stocking density of 35/decimal than that of 548 ± 178 kg/ha and 662 ± 243 kg/ha with 50 and 65/decimal respectively. The fish production (1844-1891 kg/ha) did not differ significantly (p <0.05) among the three treatments indicating that prawn stocking densities had no influence on fish yield. The lower mean harvest weight (62 g) and survival rate (67 g) and higher yield (2.67 kg/decimal) with the highest stocking rate of prawn reveals that as density was increased, prawn survival and individual weight at harvest decreased but total yield increased.