SOURCES SOUGHT
R -- REFINE FISHGRAPH SOFTWARE
- Notice Date
- 8/26/2009
- Notice Type
- Sources Sought
- NAICS
- 541690
— Other Scientific and Technical Consulting Services
- Contracting Office
- Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Eastern Region Acquisition Division-KC, 601 East 12th Street, Room 1756, Kansas City, Missouri, 64106, United States
- ZIP Code
- 64106
- Solicitation Number
- NFFN7600-9-18296SLW
- Point of Contact
- Sharon L. Walker, Phone: (816)426-7470
- E-Mail Address
-
sharon.walker@noaa.gov
(sharon.walker@noaa.gov)
- Small Business Set-Aside
- N/A
- Description
- The National Marine Fisheries Service (NMFS) Miami, FL., intends to award a sole source purchase order to the Dr. Frank Harrell, Department of Biostatistics, School of Medicine, Vanderbilt University in Nashville, TN to refine FishGraph. Fish stock assessments are population analyses used to estimate population size, age structure, and other population characteristics useful for management of exploited stocks. Assessments involve numerous graphs of input and output quantities, both for diagnostic purposes during analysis and to illustrate subsequent reports. In response to that need, Prager and co-workers developed FishGraph, an extensive set of graphing routines for assessment work. FishGraph is programmed in the R statistics environment, which makes it inherently portable and extensible. The software is currently being used at the National Marine Fisheries Service (NMFS) in Beaufort Lab for several years, and work is underway to use it at other NMFS Labs as well. Dr. Harrell is a member of the American Statistical Association and an FDA expert consultant. He is the leader of the Design, Biostatistics, and Clinical Research Ethics program for the Vanderbilt NIH and is the director of the Statistics and Methodology Core for the Vanderbilt Kennedy Center for Research on Human Development. Among his areas of emphasis are graphical and tabular methods for reporting statistical analyses. The core of this project is refinement and extension of graphics software, written in the R language that generates output compatible with the Latex markup language. Dr. Harrell has taught courses in statistical graphics and is a recognized authority in the R language, including generation of tabular and graphical output compatible with LateX. We expect that his work on the R "Hmisc" software package will be adapted to our project. By using the Vanderbilt Department of Biostatistics, we will also gain access to M.S.-level biostatisticians under Dr. Harrell's guidance, who, because of their specialized training, will be able to conduct many aspects of the work that would be difficult for those without extensive experience in R, LaTeX, and statistical graphics. The SEFSC will supply to contractor the current working FishGraph code; a beta-test version of that same code as an R package; the LateX source and PDF version of the FishGraph manual; sample data sets. Reference to "subobjects" below refer to components of the standard R list object that is the main input of each FishGraph routine, and whose structure is documented in the FishGraph manual. 1. A Google Code page has been established so that FishGraph can be distributed and discussed, and improvements proposed. The contractor shall set up this page so that it is useful to users, including the government, the contractor, and other interested parties. Security levels shall be established on the Web page so that only designated users will be able to change the FishGraph code. 2. Currently, FishGraph uses the Windows-specific R graphics function to save graphics files. Contractor shall remove this platform dependency, and any other platform dependency found, so that FishGraph can be correctly installed and used on Windows, Apple, and Linux platforms. 3. The contractor shall rework the FishGraph code as needed into an R package installable on the three platforms listed above. This will involve several steps, which shall include but not be limited to these: a. Currently, FishGraph is documented by an extensive manual. Conversion into an R package will require writing R help files for all FishGraph routines and options. Generating such files shall be done by contractor. To aid this work, SEFSC will supply Latex source code and PDF form of the current manual. b. Other scripts and file needed for packaging will be developed by contractor. c. Contractor shall provide to SEFSC a set of files and instructions that will allow SEFSC personnel, after future revisions of FishGraph code, to re-create package files under Windows. 4. Currently, FishGraph includes an R data object that stores two color models (monochrome and color), along with line types and similar graphics specifications, for use by its routines. However, those specifications are not honored by all FishGraph routines. Contractor shall extend this facility (or replace it by something similar) so that all routines use standard graphics parameters. Contractor shall provide a mechanism for the user to change standard colors if desired, and contractor shall provide user documentation as part of the R package. easier for the user to change the default colors. Implementation note: Contractor need not develop additional color models, but shall make it possible for users to substitute their own colors for FishGraph pre-defined colors in a well-documented way. We envision that, apart from extending the application of the standard color models, this task this will mainly involve documentation. 5. Contractor shall develop additional FishGraph routines to generate tabular output for use in assessment reports. Tables are needed of numbers at age (N.age subobject), total biomass at age (B.age subobject), and total mortality at age (Z.age subobject), and fishing mortality at age (F.age subobject). Two output formats shall be supported, LaTeX and CSV. a. LaTeX output: LaTeX tabular output shall include an algorithm to subdivide the tables into sections such that each section fits on an 8.5" × 11" page (with 1" margins) using no smaller than LaTeX "small" type size of the Lucida font set at 10 pt. High-level user control over subdivision is desirable but not mandatory. The tabular routines may make use of existing R add-on facilities (e.g., Hmisc package). b. CSV output shall be much simpler. The needed function shall output each of the same subobjects as an ASCII file in CSV format. Headers are required, but no other formatting or division into sub-tables is necessary. 6. Contractor shall develop, an additional graphics routine to compare population and exploitation trajectories from several model runs. The anticipated performance period is from date of award through six consecutive months thereafter. The proposed contract action is for services for which the Government intends to solicit and negotiate with only one known source, Department of Biostatistics, Dr. Frank Harrell. Interested persons may identify their interest and capability to respond to the requirement or submit proposals. This notice of intent is not a request for competitive proposals. However, all proposals received within seven days after date of publication of this synopsis will be considered by the Government. A determination by the Government not to compete with this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will normally be considered solely for determining whether to conduct a competitive procurement. All responsible sources may submit a proposal, which shall be considered by the agency. Interested firms shall include, in writing, the company name, address, point of contact, telephone number, and business size; a statement regarding their capabilities and qualifications, and any additional supporting literature. Submissions received in response to this notice shall be evaluated based on the technical ability and demonstrated past experience to meet the requirements described in the description section above. Interested parties can send requests to the attention of Sharon Walker, at fax number 816-274-6983. Vendor must provide a DUNS number (http://www.dnb.com/us/ ) and register with the Central Contractors Registration (http://www.ccr.gov/ ).
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