Integrated Analysis Tools for the NERRSSystem-Wide Monitoring Program Data
Marcus W. Beck1 Todd D. O’Brien2 Marie H. Bundy2
1USEPA NHEERL Gulf Ecology DivisionEmail: [email protected]
2NERRS/NMFS/NOAAEmails: [email protected], [email protected]
May 5, 2016
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 1 / 22
Overview
Background of National Estuarine Research Reserves (NERRS)System-Wide Monitoring Program (SWMP)
Genesis of SWMPrats.net community of practice
Features of SWMPrats.net
I SWMPr
I widgets
I forum
Continuing work, training, and engagement
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 2 / 22
What is NERRS/SWMP?
NERRSNational Estuarine Research Reserve System, established by CoastalZone Management Act of 1972. Focus on long-term research ,monitoring , education , and stewardship for more effective coastalmanagement.
SWMPSystem Wide Monitoring Program, initiated in 1995 to providecontinuous monitoring data at over 140 stations in each of the 28NERRS reserves
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 3 / 22
What is NERRS/SWMP?
http://nerrs.noaa.gov/ReservesMap.aspx
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 4 / 22
What is NERRS/SWMP?
Each reserve has fixed, continuous monitoring stations for waterquality (15 min), meteorology (15 min), and nutrients (monthly)
Water quality
temperature,conductivity, salinity,dissolved oxygen,depth, pH, turbidity,fluorescence
Meteorology
air temperature,humidity, pressure,wind speed, winddirection, PAR,precipitation
Nutrients
phosphate,chlorophyll, nitrate,nitrite, ammonium,Kjeldahl nitrogen,urea
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 5 / 22
What is NERRS/SWMP?
Data maintained by the Centralized Data Management Office (CDMO)
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 6 / 22
What is NERRS/SWMP?
As of last month, > 63 million SWMP data records available
Raw data will look like this...
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 7 / 22
What are the needs?
NERRS researchers, managers, and technicians need more tools fortrend analysis:
Understand regional and national trends while retaining theability to determine local trends
Train users
Maintain a versatile and evolving data analysis approach
Create a community of practice
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 8 / 22
Genesis of SWMPrats
One-day training workshop at 2014 annual meeting
Attended by over 70 NERRS staff, representing 19 of 28 reserves
General focus on time series analysis, simple applications withSWMP data
Pre/post workshop materials, including an R package for SWMP
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 9 / 22
Genesis of SWMPrats
A working group was formed from this meeting
System-W ide M onitoring ProgramResources for the Analysis of T ime Series
SWMPrats.net is our base of operations...
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 10 / 22
SWMPrats.net
A website with information and tools for SWMP data analysis
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 11 / 22
SWMPrats.net: The SWMPr package
SWMPr is an open-source R package described on the website, v2.1.5is now available
> # install/load from R
> install.packages('SWMPr')
> library(SWMPR)
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 12 / 22
SWMPrats.net: The SWMPr package
The software addresses the unglamorous but necessary challenges ofanalyzing time series, specific to SWMP
What are some challenges?
Dealing with ‘bad’ data
Subsetting by date ranges, parameters
Combining data from different sites
Standardizing time steps
...and analysis
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SWMPrats.net: The SWMPr package
Package description published in The R Journal this year
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SWMPrats.net: The SWMPr package
Example: fill missing data with na.approx
Tue Wed Thu Fri Sat
78
910
datetimestamp
do_m
gl
Example: smooth data with smoother
Jul 09 Jul 14 Jul 19 Jul 24
24
68
datetimestamp
do_m
gl
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SWMPrats.net: The SWMPr package
Example: time series decomposition with decomp cj (chl-a atcbmocnut)
original
annual
seasonal
events
2
3
4
5
−1.0
−0.5
0.0
0.5
−1.0
−0.5
0.0
0.5
−2
−1
0
1
2004 2006 2008 2010 2012 2014Time
valu
e
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SWMPrats.net: The SWMPr package
Example: estimate ecosystem metabolism with ecometab (apadbwq)
−10
−5
0
5
10
2012−01 2012−07 2013−01 2013−07 2014−01
Mon
thly
EstimateNEM
Pg
Rt
−10
−5
0
5
10
2012−01 2012−07 2013−01 2013−07
Qua
rter
ly EstimateNEM
Pg
Rt
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 17 / 22
SWMPrats.net: Widgets
The most common question - has there been a change over time at mysite (long-term trends)?
Three Shiny applications allow users to visualize trends in SWMP data
These apps allow ‘reactive’ use of SWMPr functions
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SWMPrats.net: Forum
Last but not least, a discussion forum for all things analytical
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Continuing work and engagement
SWMPrats.net is in its infancy but already seeing heavy use
Over 4000 visits to the website this year
3140 downloads of SWMPr to date
Apps have been used 160 hours in the last three months
Additional training workshops Oct. 2015, planned for 2016
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 20 / 22
Continuing work and engagement
SWMPrats is an ad hoc group formed organically from the NERRScommunity
Success depends on:
Healthy discourse between the creators and users
In-person training workshops
Benefits of open-source resources
M. Beck, T. O’Brien, M. Bundy NERRS Analysis Tools May 5, 2016 21 / 22
Continuing work and engagement
Contacts: [email protected], [email protected],[email protected]
To get this presentation: https://github.com/fawda123/NWQMC 16
Apps: http://swmprats.net/swmp-widgets/summary-plots,http://swmprats.net/swmp-widgets/trends-maps,http://swmprats.net/swmp-widgets/swmp-widget-aggregation
Visit the development site for the most recent version of SWMPr:https://github.com/fawda123/SWMPr
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