Statistical Support and Web Development for a Web-based Master Sample Management System for Integrating Aquatic Ecosystem Status and Trend Monitoring




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НазваниеStatistical Support and Web Development for a Web-based Master Sample Management System for Integrating Aquatic Ecosystem Status and Trend Monitoring
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Statistical Support and Web Development for a Web-based Master Sample Management System for Integrating Aquatic Ecosystem Status and Trend Monitoring

Proposal submitted to

Bonneville Power Administration

Pacific Northwest Aquatic Monitoring Partnership

Integrated Status and Trend Monitoring Workgroup


By

Statistics Department

Oregon State University


Principal Investigator

Don L Stevens, Jr.


Background: Monitoring agencies throughout the northwest are increasingly adopting the principles of survey sampling to design stream monitoring networks to track the status and trends in resource condition (stream habitat and chemistry, biota, riparian condition) for biological assessments or effectiveness of strategies. In survey sampling, sites are selected from a representation of the relevant stream networks (e.g., digital hydrographic traces) by incorporating randomization in the site selection process. Several algorithms have been developed that allow a user to select sites that meet their design requirements. An algorithm (called a generalized random-tessellation stratified design, GRTS) is increasingly being used to generate a spatially-balanced set of sites (see Stevens and Olsen (2004) and Dobbie et al. (2008) for details about the advantages of a spatially-balanced sample compared with simple random or systematic samples). One consequence of the increasing interest in using GRTS is that a variety of spatially-balanced designs are being developed in overlapping geographic domains according to each users specific interests. There is potential for redundancy, non-optimal designs, and lack of communication among agencies with overlapping responsibilities. To alleviate the potential for this type of problem and to facilitate the integration of the designs during the design process, the concept of a master sample has been developed and applied to stream networks in the NW (Larsen, et al., 2008).

A master sample is a full list of sites that could be potentially sampled, structured so that a user could select a subset from the full list and retain the principle of randomization and spatial balance in the subset of sites selected (see Larsen, et al., 2008). Statewide master samples covering stream networks in Oregon, Washington, and Idaho have been developed. A master sample file consists of a list of sites along with a set of attributes assigned to each site. Each site is identified by a unique site identifier, site latitude and longitude, and a set of design and classification attributes (e.g., initial selection weights, populations, USGS hydrologic unit code, ecoregion). Master samples can also be easily created for areas (polygons), such as estuaries, sounds, or near coastal regions.

As users become familiar with the use of a master sample, and as more and more users draw subsamples from the same master sample, a master sample tracking and management system will be necessary. Such a system will allow users to know who else has selected sites from the master sample covering stream networks in their domains; to design individual or integrated monitoring programs; to know how existing sites relate to a common master sample; and to know what others are collecting at the site over time. Such a management system could allow a user to select the part of the master sample that is relevant to his/her domain, to identify whether other users have selected subsets within their domains, and to upload information about their evaluation of the sites they selected giving future users insight into the history of sites selected within their domains. Application of the master sample concept would facilitate data sharing and integration across multiple agencies in regions of common interest, given that agreement can be reached on common protocols for indicators of common interest.

The Pacific Northwest Aquatic Monitoring Partnership (PNAMP) is developing an Integrated Status and Trends Monitoring (ISTM) project to demonstrate the concept in the Lower Columbia region. It is anticipated that the PNAMP ISTM project will increase familiarity with the concept and use of a master sample. As part of the ISTM effort, PNAMP is proposing to develop a prototype web-based master sample tracking and management system to support the interests of increasing numbers of users in drawing samples from the same population domain. This system would allow users to know who else has selected sites from the master sample covering stream networks in their domains; to design individual or integrated monitoring programs; to know how existing sites relate to a common master sample; and to know what is being collected at the site over time. In conjunction with the development and use of the web-based master sample management tool, there is a need for dedicated analytical support for design and utilization of results of the monitoring design based on the master sample. This proposal is to develop the prototype master sample management tool using the Lower Columbia region as a demonstration area and to provide the necessary statistical support. The Lower Columbia was selected as a demonstration area because it is a manageable size, several monitoring programs using GRTS designs on stream networks in the Lower Columbia are already in place, and an example area-based sample of the Lower Columbia estuary was selected by the USEPA in 2007.

This project will develop the prototype Master Sample Management System, make it available to users, and provide statistical design and analysis support for the two years of the project. This system will be developed so that it is readily expandable to more extensive regions, e.g., to the entire Pacific Northwest. At the end of the two-year project period,

Tasks

  1. Manage and administer project. This task covers all administrative and technical work to fulfill BPA's programmatic and contractual requirements such as financial reporting development of a Statement of Work (SOW) package (includes SOW and budget), and producing periodic and final reports.

  2. Develop specifications of a web-based master sample management system, and develop an implementation plan. The project will develop a prototype of a web-based master sample management system. It will be necessary to explore with the web developer the various web-based systems and options to meet the desired capabilities. With the advice and input of PNAMP, a small workgroup will be established to define the details of the prototype and to ensure seamless integration with other PNAMP web-based applications. The work group will consist of a statistician, a web developer, and representatives from various federal agencies (e.g. PNAMP, USEPA, NOAA), state agencies (e.g., ODFW, WA ECY), and other interested parties (e.g., LCREP, Pacific States Marine Fisheries Commission). The group will define operational attributes of the master sample management system. As the project develops, continual interaction between the work group and the web developer will be necessary to evaluate progress, explore the draft web-based capabilities, and ensure that the project is proceeding in a desired direction.

  3. Regional Coordination. The project will actively seek to establish partnerships to ensure compatibility of the system with existing state- or region-wide master sample management tools. For example, a Master Sample of streams already exists for Washington State, and the Washington State Department of Ecology (WA-ECY) has made it available on-line. However, the system, as currently configured, allows subset selection only by Water Resource Inventory Area, not by any other classification variable such as stream order. Moreover, there is no functionality that would allow a user to submit information about their designs and the status of the master sample sites that they drew from the web. This project intends to coordinate with agencies like ECY to insure that the web-based prototype is compatible with their systems.

  4. Develop a prototype web-based master sample management system. Development of the web-based prototype will occur based on the specifications established in Task 2. We anticipate that this system will have at least the following capabilities:

  • Store master samples and associated metadata (e.g., design documentation) on a readily accessible server;

  • Allow users to download relevant parts of the master sample;

  • Allow users to upload information about master sample sites that they have evaluated (to include design documentation, site evaluation, indicators measured, protocols used);

  • Provide a tracking system that documents the history of sites selected from the master sample;

  • Allow users to download histories of previously selected sites (to include design documentation, site evaluation, indicators measured, protocols used);

  • Allow scaling up to a statewide, or multi-state system (this primarily means the capability to manage substantially larger master samples than that used for the prototype);

  • Ensure protection of data (via a secure system);

  • Provide a mapping tool to display master sample sites selected by previous users.

  1. Create Master Sample for the Lower Columbia. As noted above, several GRTS sample designs already exist in the Lower Columbia region. Methodology for merging an existing sample with additional sites has been developed by the StatNat Group at Oregon State University and applied to the Oregon Department of Fish and Wildlife’s coastal coho monitoring program. This methodology will be used to integrate these existing sites with newly selected random sites to produce a high-density, spatially-balanced GRTS sample. In addition, the USEPA selected a high-density area-based sample of the Lower Columbia estuary in 2007. This sample will be reviewed and if suitable, will be used for the area-based master sample of the estuarine portion of the Lower Columbia.

  2. Provide statistical oversight as the web tool is developed. One of the benefits of a web-based Master Sample implementation is that it provides access to rigorous statistical sampling designs for any organization monitoring the Master Sample population. To maintain that statistical rigor, the web-based tool must be developed with close cooperation between the tool developers and statisticians familiar with the GRTS technique. The principles underlying the application of the Master Sample are well-understood, and Larsen, et al., (2008) present some examples of selecting focused samples from the Master Sample using ancillary information. However, implementation of a variety of design options, for example, stratification, rotating panels, and oversamples, will require statistical oversight. Furthermore, the web tool should be developed to facilitate eventual analysis of the sample selected. There must be a clear path for users to follow from design specification to sample selection to data collection, input, and analysis. One of the critical elements in that path is the automatic production of a design documentation file. This file documents the selection process so that appropriate inclusion probability or weight and other sample structure (e.g., stratification, panels) will be available for analyzing the data collected at the sample sites. The content and format of the file will be developed jointly by the web developer and the statisticians with input from the workgroup. Additionally, efforts under PNAMP to develop and capture metadata related to statistical and monitoring design, data collection and analysis will inform the format of design documentation developed under this task.

  3. Identify needs and develop web-based analysis tools. Another critical element is the development of tools that will link the design files with field data to provide easy access to analysis tools. It is important that these tools meet the analytical needs of ISTM major partners (e.g., OR and WA recovery plans, AREMP, etc), and that they are commensurate with standards developed by PNAMP and the Integrated Status and Effectiveness Monitoring Program (ISEMP). For example, the R package spsurvey developed by the USEPA already has tools for routine analysis of GRTS survey data, but there is a need to develop an interface to interact with these. Moreover, additional analysis tools are available that have not been implemented in spsurvey, and others, notably analysis of trend from rotating panel studies, will become available shortly. These tools will be made available as a part of the overall Master Sample implementation.

  4. Provide statistical consultation support to assist users with complex sampling issues. The intent of the Master Sample web tool is to simplify application of rigorous statistical monitoring designs and analyses. Documentation will be provided that will facilitate most applications; however, the tool will have the capability to create designs to satisfy very complex requirements. For complex designs, users may need to consult with a statistician familiar with the Master Sample management system to meet design requirements.

  5. Develop and implement methodology for combining data from non-probability monitoring (e.g., index sites) with data from statistical surveys. Historically, much monitoring data was collected without a formal probability design. Combining such non-probability data with data from a probability survey can be difficult because of the lack of unambiguous link between the data and population representation. Several methods (Brus & De Gruijter, 2003; Overton et al., 1993; Stein & Bernstein, 2007) have been proposed, and the applicability and feasibility of these will be evaluated and implemented accordingly.

  6. Develop training materials and user guides. This task will provide detailed documentation of the steps required to select a design, annotated examples of particular applications, guidance for selecting analysis procedures, and annotated examples of applying the analysis tools.

  7. Present seminars/workshops on use of Master Sample management system. The intent of the project is to make the management system user-friendly; nevertheless, we foresee the need to communicate and encourage its application by providing some introductory training via presentations, seminars, and/or workshops. This task will be coordinated through PNAMP.



Products/Deliverables: The project will produce:

  1. A prototype web-based master sample management system that is fully functional on the Lower Columbia region

  2. Lower Columbia Master Sample

  3. Statistical package in the R language interfaced with the management system that provides basic analysis of master samples

  4. Statistical support to users to assist with meeting complex design requirements and subsequent analysis

  5. Documentation and users guides for the system

  6. Delivery of seminars/workshops on use of master sample management system.


Project Personnel

Senior Statistician: Don L. Stevens, Jr. is Senior Research Professor in the Statistics Department at Oregon State University (OSU). Dr. Stevens is an internationally known environmental statistician, particularly in the area of environmental sampling and monitoring. He is a Fellow of the American Statistical Association, an elected member of the International Statistical Institute, and President-elect of The International Environmetrics Society. He made fundamental contributions to developing the statistical sampling theory supporting EMAP’s spatially-balanced probability sampling, and applying that theory to designing samples of a variety of aquatic resources. Dr. Stevens has supervisory and project management experience, both in academia and contract research. While at Eastern Oregon State University, he was Area Coordinator for Mathematics and Computer Science, and Principal Investigator on a cooperative agreement from USEPA to develop the sampling design for the Direct-Delayed Research Project. Subsequently, he held positions as a General Supervisor and Project Manager for two on-site contractors at the USEPA Laboratory in Corvallis. At OSU, he was the Program Director for the EPA-STAR-funded Program on Designs and Models for Aquatic Resource Surveys. He is a consultant on environmental monitoring design issues for the Warm Springs Indian Tribe, the National Parks Services Great Lakes Monitoring Network, the San Francisco Estuary Regional Monitoring Program, California’s Surface Waters Ambient Monitoring Program, California’s Fish Mercury Program, the Oregon Department of Fish and Wildlife, the Oregon Watershed Enhancement Board, and Australia’s Commonwealth Science and Industrial Research Organization Environmental Informatics group.

Statistician: Lisa Madsen is an Assistant Professor in the Statistics Department at OSU. Dr. Madsen’s research focuses on spatial data and problems in environmental and ecological statistics. Her dissertation addressed the problem of spatially misaligned data. Since then, she has been working with dependent, non-Gaussian ecological data problems, particularly count data with many zero counts. She has expertise in simulating ecological data. She is director and co-founder of StatNat (Statistics for Natural Resources), a group of statisticians at Oregon State University working on problems in natural resources monitoring. StatNat has close working relationships with the Oregon Department of Fish and Wildlife, the Oregon Department of Forestry, and the Oregon Watershed Enhancement Board.

Web Developer / Systems Engineer: Clifton Johnson has over twenty years experience in the IT field, including six in his current role at Oregon State University. While at Oregon State University (OSU), Clifton has been involved in developing online websites and specific applications (including online surveys, and data processing systems which utilize the open source R application, php and mysql database backends) as well as providing support, custom programming, database design/management and server administration (primarily focusing on the linux operating system). Clifton has an interest in, and a preference for, the development and use of open source applications, and was instrumental in the adoption of Drupal (http://www.drupal.org) as a standard Content Management System (CMS) web framework, which has been used for many of the websites on campus. In addition to his web development and systems administration duties, Clifton assists researchers utilize a Beowulf cluster to more efficiently process data or run simulations.


References

Brus ,D. J., and J. J. De Gruijter. 2003. A method to combine non-probability sample data with probability sample data in estimating spatial means of environmental variables. Environmental Monitoring and Assessment 83: 303–317, 2003.

Dobbie, M.J., B.L. Henderson, and D.L. Stevens, Jr. 2008. Sparse sampling: Spatial design for monitoring stream networks. Statistics Surveys 2:113-153.

Larsen, D.P., A.R. Olsen, and D.L. Stevens, Jr. 2008. Using a master sample to integrate stream monitoring programs. Journal of Agricultural, Biological, and Environmental Statistics 13:243-254.

Overton, J., T. Young, and W.S. Overton. 1993. Using ‘found’ data to augment a probability sample: procedure and case study. Environmental Monitoring and Assessment. 26:65–83.

Stein, E.D., and B. Bernstein. 2008. Integrating probabilistic and targeted compliance monitoring for comprehensive watershed assessment. Environmental Monitoring and Assessment 144:117–129

Stevens, D.L., Jr. and Olsen, A.R. 2004. Spatially-balanced sampling of natural resources. Journal of American Statistical Association 99: 262–278. Oregon State University


Budget

Budget Period: 1 June 2009 – 30 Sept 2009

Personnel




Senior Statistician (4 mo @0.9 FTE @ $10,525/mo)

$37,890

OPE 37%

14,019

Statistician (2 mo @ 0.5 FTE @ $7,141/mo)

7,141

OPE 25% (note 1)

1,785

Web Developer (560 hours @ $50/hour, OPE included)

28,000

Sub-total personnel

$83,068







Office Supplies




Miscellaneous paper, postage, computer supplies

$100







Travel




POV (4 round trips to Portland @200 mi/trip @ $0.55/mi

$440







Total Direct Cost

$88,375







Facilities & Administration




46.2 % TDC

$41,291







Total Cost – Budget Period 1

$130,666

Notes: (1) summer rate for 9-mo faculty


Budget Period 2: 1 Oct 2009 – 30 Sept 2010

Personnel




Senior Statistician (3 mo @0.8 FTE @ $10,525/mo)

$22,103

OPE 37%

8,178

Senior Statistician (9 mo @0.05 FTE @ $10,525/mo)

4,736

OPE 10% (note 1)

474

Statistician (2 mo @ 0.1 FTE @ $7,855/mo)

1,571

OPE 25% (note 2)

393

Web Developer (890 hours @ $52/hour, OPE included)

46,280

Sub-total personnel

$83,735







Office Supplies




Miscellaneous paper, postage, computer supplies

$200







Travel




POV (8 round trips to Portland @200 mi/trip @ $0.55/mi

$880







Total Direct Cost

$84,815







Facilities & Administration




46.2 % TDC

$39,185







Total CostBudget Period 2

$124,000

Notes: (1) 1040 appointment rate; (2) summer rate for 9-mo faculty


Budget Period 3: 1 Oct 2010 – 30 May 2011



Personnel




Senior Statistician (8 mo @0.05 FTE @ $10,946/mo)

$4,378

OPE 10%

438

Web developer(50 hours @ $54/hour, OPE included)

2,700

Sub-total personnel

$7,516







Office Supplies




Miscellaneous

$100







Travel




POV (4 round trips to Portland @200 mi/trip @ $0.55/mi

$440







Total Direct Cost

$8,056







Facilities & Administration




46.2 % TDC

$3,722







Total CostBudget Period 3

$11,778







Total Project Cost

$266,444




Budget Breakout by Task

Task

Cost

1. Manage and Administer Project

$9,000

2. Produce Plan

24,000

3. Regional Coordination

5,000

4. Develop a prototype web-based master sample management system

112,544

5. Create Master Sample for the Lower Columbia

24,000

6. Provide statistical oversight as the web tool is developed

9,900

7. Identify needs and develop web-based analysis tools

30,000

8. Provide statistical consultation support to assist users with complex sampling issues.

15,000

9. Develop and implement methodology for combining data from non-probability monitoring (e.g., index sites) with data from statistical surveys

22,000

10. Produce user’s guide and training materials

10,000

11. Present seminars and/or workshops on use of master sample management system


5,000

Total

$266,444



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