class: center, middle, inverse, title-slide # OPEN SCIENCE AT TBEP: TIDAL TRIBUTARIES EXAMPLE ###
Dr. Marcus Beck
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@fawda123
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#TampaBayOpensci
### TAMPA BAY ESTUARY PROGRAM ### July 8th, 2020 --- class: top, middle <style> .remark-code, .remark-inline-code { font-family: 'Source Code Pro', 'Lucida Console', Monaco, monospace; font-size: 70%; } </style> ## TODAY'S GOALS .left[ * A quick primer on open science (__excite!__) * How we are using open science at TBEP (__understand!__) * Using open science to assess tidal tributaries (__show!__) ] .center[ ### __*How can you (I) help me (you) create better science in less time?*__ ] --- class: middle, center, inverse # Open Science 101 --- class: middle, center ## The research-management divide <img src="figure/divide2.png" width="100%" /> --- class: middle, center <img src="figure/michener.png" width="90%" /> .footnote[Michener et al. 1997 Ecol. App. 7(1):330-342.] --- class: middle, center ## Open science can bridge this divide <img src="figure/bridge.png" width="100%" /> --- class: middle, center ### The practice of science in such a way that others can **collaborate** and **contribute**, where research data, lab notes and other research processes are **freely available**, under terms that enable **reuse**, **redistribution** and **reproduction** of the research and its underlying data and methods .footnote[Open Knowledge International, [http://opendefinition.org/](http://opendefinition.org/), [https://creativecommons.org/](https://creativecommons.org/about/program-areas/open-science/)] --- class: middle, center #
Open data #
Open process #
Open products --- class: middle, center, inverse # An example... --- class: top, center ## WATER QUALITY REPORT CARD .pull-left[ <img src="figure/wqstatic1.PNG" width="100%" /> ] .pull-right[ <img src="figure/wqstatic2.PNG" width="100%" /> ] --- class: top, center ## THE OLD (closed) WAY <img src="figure/badflow2.png" width="100%" /> --- class: top, center ## THE NEW (open) WAY <img src="figure/flow3.png" width="100%" /> --- class: top, center ## THE NEW (open) WAY .left[ * Transparent and reproducible methods * Discoverable products that can engage others * Automated data QAQC and integration with reporting * New front-facing web products, both static and interactive ] --- class: middle, center ## THE LOW HANGING CCMP INDICATORS <img src="figure/tree.png" width="30%" /> .pull-left[ ####
WATER QUALITY REPORT CARD ####
BENTHIC INDEX ] .pull-right[ ####
NEKTON INDEX ####
TIDAL CREEK ASSESSMENT ] --- class: top, center ## TIDAL CREEK ASSESSMENT .pull-left[ <img src="figure/tidalcreekreport1.PNG" width="100%" /> ] .pull-right[ <img src="figure/tidalcreekreport2.PNG" width="100%" /> ] --- class: top, left .center[ ## TIDAL CREEK ASSESSMENT ] * Evaluates relative exceedances of nitrogen concentrations as a quantitative stressor * Assumes nitrogen has link to health of fish community * Includes temporal component to evaluate change over time * Multiple other indicators provide context --- class: top, left .center[ ## TIDAL CREEK ASSESSMENT ] <img src="figure/crkflo1.png" width="100%" /> <img src="figure/crkflo2.png" width="100%" /> --- class: top, left .center[ ## TIDAL CREEK ASSESSMENT ] <img src="figure/crkflo3.png" width="100%" /> <img src="figure/crkflo4.png" width="100%" /> --- class: top, left .center[ ## TIDAL CREEK ASSESSMENT ] ### Creeks assigned to categories within a management framework: <span style="color:#33FF3B; text-shadow: 0 0 3px #333;">__Target__</span>: Creek is at or below nitrogen concentrations that protect individual creek types within the larger population of creeks. <span style="color:#F9FF33; text-shadow: 0 0 3px #333;">__Caution__</span>: Creek nutrients showing signs of eleveted nutrient concentrations that may increase risk of eutrophic condition. <span style="color:#FFA500; text-shadow: 0 0 3px #333;">__Investigate__</span>: Creek nutrient concentrations above margin of safety to protect creek from potential impairment. <span style="color:#FF7F50; text-shadow: 0 0 3px #333;">__Act__</span>: Creek nutrient concentrations have exceeded regulatory standard for associated freshwater portion of tributary indicating that actions are needed to identify remediative measures to reduce nutrients to the creek. --- class: middle, center # FOR EVERY INDICATOR, A NEW WORKFLOW --- class: top, left .center[ ## TBEPTOOLS R PACKAGE ] * Import raw data, estimate indicators, and report outcomes * Foundational methods for indicator reporting * Freely available on GitHub for anyone to view source code, download for use, and make requests for additions <img src="figure/tbeptoolshex.png" width="20%" style="display: block; margin: auto;" /> .center[ [https://tbep-tech.github.io/tbeptools/](https://tbep-tech.github.io/tbeptools) ] --- class: top, left .center[ ## IT'S SUPER SIMPLE... ] ```r results <- anlz_tdlcrk(tidalcreeks, iwrraw) results ``` ``` ## # A tibble: 580 x 10 ## id wbid JEI name class target caution investigate act score ## <int> <chr> <chr> <chr> <chr> <int> <int> <int> <int> <chr> ## 1 1 2052 CC01 Rock Creek 3M NA NA NA NA No Da~ ## 2 2 1983B CC01 Rock Creek 2 NA NA NA NA No Da~ ## 3 3 1983B CC02 Oyster Creek 2 1 NA NA NA Target ## 4 4 2067 CC02 Oyster Creek 3M 1 NA NA NA Target ## 5 5 1983B CC03 Buck Creek 2 NA NA NA NA No Da~ ## 6 6 2068 CC03 Buck Creek 3M NA NA NA NA No Da~ ## 7 7 2078A CC04 Buck Creek 2 2 NA NA NA Target ## 8 8 2078B CC05 Coral Creek 2 2 NA NA NA Target ## 9 9 2078A CC05 Coral Creek 2 NA NA NA NA No Da~ ## 10 10 2065C CC06 Catfish Creek 2 NA NA NA NA No Da~ ## # ... with 570 more rows ``` --- class: top, left .center[ ## IT'S SUPER SIMPLE... ] ```r show_tdlcrk(results) ```
--- class: top, center ## TIDAL CREEKS DASHBOARD <img src="figure/tidalcreekdash2.PNG" width="100%" style="display: block; margin: auto;" /> [https://shiny.tbeptech.org/tidalcreek-dash/](https://shiny.tbeptech.org/tidalcreek-dash/) --- class: top, left .center[ ## TIDAL CREEKS DASHBOARD ] * Interactive summaries of creek condition by user selection * Additional context indicators for each creek * Figure and data downloads * Full documentation .center[ [https://shiny.tbeptech.org/tidalcreek-dash/](https://shiny.tbeptech.org/tidalcreek-dash/) ] --- class: top, middle ## TODAY'S GOALS .left[ * A quick primer on open science (__excite!__) * How we are using open science at TBEP (__understand!__) * Using open science to assess tidal tributaries (__show!__) ] ### __*How can you (I) help me (you) create better science in less time?*__ --- class: top, center ## GET INVOLVED .left[ * An application must meet the needs of those that require science to inform decisions * Development requires two-way exchange of ideas ] ### __*How could managers use these data?*__ ### __*How could these products support policy?*__ ### __*Join the open science subcommittee!*__