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 market for Egyptian farmed fish

Egypt’s aquaculture production (921,585 tonnes in 2010) is by far the largest of any African country. The aquaculture sector, dominated by semi-intensive pond production of tilapia, makes a significant contribution to income, employment creation and food and nutrition security in the country, all of which are national priority areas given low per capita income levels, rising population, worsening food and nutrition security indicators, and official unemployment levels which have remained at around 10% for the last ten years. The Improving Employment and Income through Development of Egypt’s Aquaculture Sector (IEIDEAS) project funded by the Swiss Agency for Development and Cooperation (SDC) is a three-year project which commenced in December 2011, and which aims to support the development of the aquaculture sector in Egypt so as to increase productivity, profitability, and employment in the sector, and the nutritional status of poor consumers. This report represents the output of a short two-week study to better understand the market for Egyptian farmed fish. The intention of the study was to provide an output which would cut-across, and potentially benefit, all five of the project outcomes.

Institutional, policy and regulatory framework for sustainable development of the Egyptian aquaculture sector

This report presents the findings of a mission to critically review the institutional, policy and regulatory framework for sustainable development of the Egyptian aquaculture sector. The study was undertaken by an International Expert on Aquaculture Policy, and a National Expert on Institutions, on behalf of the Project “Improving Employment and Income through the Development of Egypt’s Aquaculture Sector“, implemented by WorldFish and CARE, and funded by the Swiss Agency for Development and Cooperation(SDC). The objective of the mission was to assess the current status of the Egyptian aquaculture sector, in terms of the policy, legal and institutional environment, with a view to suggesting the major issues to be addressed within a future policy dialogue.

Value chain analysis of the Egyptian aquaculture feed industry

The commercial aquaculture feed industry in Egypt is growing at a rapid rate. As a result, the number of fish feed mills has increased from just 5 mills producing about 20,000 t per year in 1999, to over 60 mills with a current production estimate of 800,000–1,000,000 t/year. The performance of the aquafeed industry in Egypt is not well understood, as the value chain structure has not yet been mapped. This study aims to assess the status of the fish feed sector in Egypt, with an emphasis on: mapping and understanding fish feed value chains, describing the main actors and stakeholders within the chain, assessing value chain performance, identifying major strengths and weakness of the sector, and suggesting appropriate actions, management and development strategies.

Circulation pattern of the Egyptian Mediterranean waters during winter and summer seasons

The water circulation of the Egyptian Mediterranean waters was computed during winter and summer seasons using the dynamic method. The reference level was set at the 1000db surface. The results showed that the surface circulation is dominated by the Atlantic water inflow along the North African coast and by two major gyres, the Mersa Matruth anticyclonic gyre and El-Arish cyclonic gyre. The results showed a seasonal reversal of El-Arish gyre, being cyclonic in winter and anticyclonic in summer. El-Arish gyre had not been previously measured. The geostrophic current velocity at the edges of the Mersa Matruth gyre varied between 12.5 and 29.1cm/sec in winter and between 6.5 and 13.1cm/sec in summer. The current velocity reached its maximum values (>40cm/sec) at El-Arish gyre. The current velocity at the two gyres decreased with increasing depth. The North African Current affects the surface waters down to a depth of 100m, and that its mean velocity varies between 6 and 38cm/sec.