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)

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.

The Computer Input/Output Subsystem Education in an undergraduate introductory course: a Multiperspective Study

240 p.

Investigation of transient process and steady output of lasing without inversion

The transient evolution processes and steady outputs of continuous wave lasing without inversion (LWI) and self-pulsing LWI in a resonant open V type three-level system are studied. It was found that the two kinds of LWI have some obvious differences not only from the steady outputs but also from the transient evolution processes. The effects of the unsaturated gain coefficient, cavity loss coefficient, ratio of the atomic injection rates and atomic exit rate on the transient evolution processes and steady outputs are discussed.

Quantum superchemistry in an output coupler of coherent matter waves

We investigate the quantum superchemistry or Bose-enhanced atom-molecule conversions in a coherent output coupler of matter waves, as a simple generalization of the two-color photoassociation. The stimulated effects of molecular output step and atomic revivals are exhibited by steering the rf output couplings. The quantum noise-induced molecular damping occurs near a total conversion in a levitation trap. This suggests a feasible two-trap scheme to make a stable coherent molecular beam.