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)

Temporal trends (2000–2011) and influences on fishery-independent catch rates for loggerhead sea turtles (Caretta caretta) at an important coastal foraging region in the southeastern United States

Seasonal trawling was conducted randomly in coastal (depths of 4.6–17 m) waters from St. Augustine, Florida, (29.9°N) to Winyah Bay, South Carolina (33.1°N), during 2000–03, 2008–09, and 2011 to assess annual trends in the relative abundance of sea turtles. A total of 1262 loggerhead sea turtles (Caretta caretta) were captured in 23% (951) of 4207 sampling events. Capture rates (overall and among prevalent 5-cm size classes) were analyzed through the use of a generalized linear model with log link function for the 4097 events that had complete observations for all 25 model parameters. Final models explained 6.6% (70.1–75.0 cm minimum straight-line carapace length [SCLmin]) to 14.9% (75.1–80.0 cm SCLmin) of deviance in the data set. Sampling year, geographic subregion, and distance from shore were retained as significant terms in all final models, and these terms collectively accounted for 6.2% of overall model deviance (range: 4.5–11.7% of variance among 5-cm size classes). We retained 18 parameters only in a subset of final models: 4 as exclusively significant terms, 5 as a mixture of significant or nonsignificant terms, and 9 as exclusively nonsignificant terms. Four parameters also were dropped completely from all final models. The generalized linear model proved appropriate for monitoring trends for this data set that was laden with zero values for catches and was compiled for a globally protected species. Because we could not account for much model deviance, metrics other than those examined in our study may better explain catch variability and, once elucidated, their inclusion in the generalized linear model should improve model fits.

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 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.