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U.S. EPA - ORD.NHEERL Atlantic Ecology DivisionNarragansett, Rhode Island
Hal Walker [email protected]
Estuary and Coastal Conditions Reporting
Got Data? - Cool Tools for Effective Data Presentation
New England Regional Volunteer Monitoring WorkshopFriday, November 16th, 2007
EPA New England Regional Laboratory
North Chelmsford, MA
Got Data? - Cool Tools for Effective Data PresentationSuggested components of presentation
1. Quick intro to what your program is:
National Coastal Assessment: http://www.epa.gov/emap/nca/
2. Rationale for developing an index (why created)
National consistency in reporting on estuarine condition
3. Mechanics of the index (not too much detail – but hopefully with information on how to get more information)
NCCR2 http://www.epa.gov/owow/oceans/nccr/2005/Chapt1_Intro.pdf
4. Examples of how index has been used or will be used
National Coastal Condition Reports http://www.epa.gov/owow/oceans/nccr/
5. How successful has it been
Outstanding Achievement Award Renewable Natural Resources Fund
6. Lessons learnedConsistency in goals, rational, approach, funding. Partnership with States and Tribes key to success. Tech transfer of methods / reproducibility
2
• Report Cards (Medical example and Watershed Example)
• National Coastal Assessment Overview (indicators and indices) • Example Regional Scale Results (water quality indicators)• Example State Level reporting (sediment quality index)
• “Cool tools” Philosophy (Reproducible Calculations / Flexibility)• Computational Approaches (ArcMap, Excel, R-Excel, R script)
Excel example, R-Excel example
• Next steps (adapt computation tools for lakes assessments)
Got Data? - Cool Tools for Effective Data Presentation: Defining the Goal, Audience, Computational & Reporting Methods
3
Talk Outline:
• My son was diagnosed with leukemia at age 6 What are the indicators ? Do we need additional information on cell type? What are the treatment options ?
• Your watershed has problems. What are the indicators and indices of condition ? Do we need more monitoring information ?
How do we inform the decision making process ?
How doctors think. Dr. Jerome Groopman NPR audio interview http://
www.npr.org/templates/story/story.php?storyId=8892053
Defining the Goal, Audience, Computational & Reporting Methods
Have Data: How do we present the data to decision makers ?
4
SAMPLES
GENESDiscrimination between two forms of Leukemia: ALL, and AML
From Goulb et at (1999)
Heatmap.
based on gene expression monitoring by DNAMicroarrays. Automatically discovered the AML / ALL distinctions.
ALL
AML
Predicted vs Observed
This analysis is reproducible using open source R software http://www.bioconductor.org/docs/papers/2003/Compendium/Golub.pdf
Goal for report components: (1) Report, (2) Data, (3) Computational Script
“Smart Monitoring: The River is the Report Card for the Watershed” from Warren Kimball, MA DEP
6
• Report Cards (Medical example and Watershed Example)
• National Coastal Assessment Overview (indicators and indices) • Example Regional Scale Results (water quality indicators)• Example State Level reporting (sediment quality index)
• “Cool tools” Philosophy (Reproducible Calculations / Flexibility)
• Computational Approaches (ArcMap, Excel, R-Excel, R script)
Excel example, R-Excel example• Next steps (Adapt computation tools for lakes assessments)
Got Data? - Cool Tools for Effective Data Presentation: Defining the Goal, Audience, Computational & Reporting Methods
7
Assess the ecological condition of estuarine resources. Based on unbiased data of know quality
Determine reference conditions for studies on ecological responses / stressors.
Build infrastructure in states and EPA Regions.
National Coastal Assessment (NCA) is working in National Coastal Assessment (NCA) is working in partnership with States Regions and Tribes to:partnership with States Regions and Tribes to:
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Estuarine Assessment & Reporting involves partnerships: EPA ORD NHEERL & OW, NOAA & NMFS, USGS, Fish and Wildlife Service, Coastal States, and Universities
http://www.epa.gov/emap/nca/
Reporting on conditions in Nation’s estuaries and Large Marine Ecosystems
Improvement in consistency in assessments required by the Clean Water Act (CWA)
9
National Coastal Condition Reports (NCCRs) are based on probability survey and advisory data from regulatory agencies
Large Marine Ecosystems (LMEs)
NCA receives EPA ORD “Team Work Award”, 2007
Offshore surveys
10
http://www.epa.gov/owow/oceans/nccr/
NCA Partners in Northeast
Chesapeake BayProgram
Suffolk CountyDHS
AED receives ORD Statesmanship Award, 2002
11
sampling designs by water body
States share sampling
regional data sharing
frequent meetings
Approach:
Utilize consistently measured indicators to assess and help explain estuarine condition
Utilize Probability surveysExtrapolates to all of estuarine watersAddresses 305(b) requirements & GPRA100% assessed waters
Incorporate existing monitoring programs, & develop hybrid monitoring designs
National Coastal AssessmentNational Coastal Assessment
12
• Surveys in the Northeast estuaries from 2000 thru 2006
• Production of a series of National reports
• Technology transfer from EPA ORD to EPA Regions, Office of Water, States and Tribes
• Data sharing within the Northeast Region
• Use of environmental indicators, indices, and tech transfer of “computational tools”
National Coastal AssessmentNational Coastal Assessment
13
Analysis and Reporting
National Coastal Condition Reports
National Estuary Program Coastal Condition Report
In Nov 2007 U.S. EPA National Coastal Assessment to receive “Outstanding Achievement Award” Renewable Natural Resources Fund
14
http://www.epa.gov/owow/oceans/nccr/
Water Quality
- dissolved oxygen- salinity- temperature- pH- depth- light attenuation- secchi depth- dissolved nutrients- chlorophyll a- total suspended solids (TSS)
Sediment Quality- sediment contaminants . (organics & metals)- sediment TOC- sediment toxicity (amphipod)- percent silt/clay
Biota Fish/Shellfish-community structure (fish)- tissue contaminants (organics & metals)- external pathology (fish)
Benthos- community structure
Habitat - SAV (presence/absence)
west coast & gulf coast- basic habitat type
(e.g., open water, tidal flat)- marine debris (presence/absence)
Consistently Measured Indicators Consistently Measured Indicators Coastal 2000 / NCA Core Indicators:Coastal 2000 / NCA Core Indicators:
Not Measured by NCA
- SAV SAV condition
-Macro algal biomass-Harmful algal blooms-Biomass of sensitive and
tolerant taxa
15
National Coastal Assessment in Northeast(random locations in 2000 survey)
16
Findings Exceeded chronic
criterion for DO in stratified water south of Cape Cod
National Coastal Assessment: Regional Characterization Probabilistic sampling design / Summer 2000.
NO2- + NO3
-
Secchi depth Sigma-T
Dissolved Oxygen
Quartiles
Chlorophyll-a
New England SPARROW Model Output
TN Loading (estimated annual means)
Narragansett Bay
Water Quality Example
17
Estuarine water quality indicators
18
National Coastal Condition Report IINational Coastal Condition Report II( lots of indicators rolled up into 5 indices, with additional assessment info )( lots of indicators rolled up into 5 indices, with additional assessment info )
Indicators used in 5 indices, rolled up to National statement of condition
5 Indices
Overall Regional Coastal Conditions
19
National Coastal Assessment Northeast (2000) (a look at estuarine water quality indicators)
20
21
22
23
24
1) Sediment toxicity
2) Sediment Contaminants
3) Total Organic Carbon
Sediment Quality Indicators
25
Sediment Condition Index 3 indicators rolled into 1 sediment condition index
1)
2)
3)
26
An example of New Jersey DEP web-based reporting on estuarine Sediment Condition Index and indicators:
http://www.state.nj.us/dep/wms//bmw/NCA/NCAmain.htm27
http://www.state.nj.us/dep/wms//bmw/NCA/NCASediment.html
Move cursor over pie diagram and click
28
http://www.state.nj.us/dep/wms//bmw/NCA/SedQualDelaware.htm
Select Sed Quality component and click, e.g. Sed contaminants.
29
http://www.state.nj.us/dep/wms//bmw/NCA/SedChemDelaware.htm
Select site of interest, and click
30
http://71.59.88.199/SondePages/BuildSedChemTable.php?Loc=DE01-0074
Website uses Open Source code (PHP) scripting language for web development http://www.php.net/ to query a MySQL database (easy to share with collaborators)
31
• Report Cards (Medical example and Watershed Example)
• National Coastal Assessment Overview (indicators and indices) • Example Regional Scale Results (water quality indicators)• Example State Level reporting (sediment quality index)
• “Cool tools” Philosophy (Reproducible Calculations / Flexibility)• Computational Approaches (ArcMap, Excel, R-Excel, R script)
Excel example. Conditional Probability (R-Excel example).
• Next steps (Adapt computation tools for lakes assessments)
Got Data? - Cool Tools for Effective Data Presentation: Defining the Goal, Audience, Computational & Reporting Methods
32
Statistical Analysis Tools
• Excel & R-Excel• Conditional Probability Analysis
GIS Visualization Tools• ArcMap projects• ArcGIS server in the works
Northeast Partners can reproduce and refine analyses
Partners can re-compute (point and click) summary statistics and visualize regional and local multivariate data structures
33
http://www.epa.gov/emap/nca/html/regions/er/index.html Public Access: http://www.epa.gov/emap/nca/html/regions/northeast.html
Password protected website for NCA partners
Making data analysis & visualization reproducible
Computational tools: Excel: regional & State maps,
% area statistics, state comparisons
ArcMap projects for spatial visualization
• Narragansett Bay biota (map below)
Diagnostics• e.g. other contaminants at Hg hot spot Ratios of site specific chemical
concentrations to regional medians
Mercury in Rhode Island sediments
Biotic conditions in upper Bay
Narragansett Bay
Mercury “hot spot”
34
Pro
bab
ility
of
Imp
airm
ent
usi
ng
CB
P B
-IB
I Acute criteria
Chronic criteria
Conditional probability calculated using an Excel plug in
Associating biotic conditions with stressors
What “reference levels” are protective?
Dissolved oxygen example
Distribution of the Chesapeake Bay Program’s Benthic Index of Biotic Integrity (CBP B-IBI) Scores as a Function of Bottom Dissolved Oxygen Concentrations (mg/L)
35
Statistical Analysis Tools
• Excel • Conditional Probability Analysis
GIS Visualization Tools• ArcMap projects• ArcGIS server in the works
Partners can reproduce and refine analyses
Partners can re-compute (point and click) summary statistics and visualize regional and local multivariate data structures
36
EPA Portal
Allows for remote desktop sharing http:\\portal.epa.gov
(for download Google “CProb EPA”)
An important “turn of the century” baseline
A conceptual framework, and approach for addressing Agency needs
National Condition
Accountability
Acute criteriaChronic criteria
Pro
bab
ility
of
Imp
airm
ent
usi
ng
CB
P B
-IB
I
Standards
Site specific diagnostics
Ele
ctro
nic
Rep
orts
37
Reproducible Research