class: center, middle, inverse, title-slide # Hydrology and chlorophyll trends in Tampa Bay: Alternative modelling approaches ### <a href="mailto:mbeck@tbep.org">Dr. Marcus Beck</a> <span class="math inline">•</span> <a href="https://twitter.com/fawda123">@fawda123</a> <span class="math inline">•</span> <a href="https://twitter.com/hashtag/TampaBayOpenSci?src=hashtag_click">#TampaBayOpensci</a> ### Tampa Bay Estuary Program ### 10/16/2020 --- class: middle, center, inverse # Our last discussion... --- class: center, top # Reporting requirements and products <div class="container"> <div class="column-left"><img src="figure/decisionframework.png" width = "340"></img></div> <div class="column-center"><img src="figure/wqstatic1.PNG" width = "340"></img></div> <div class="column-right"><img src="figure/wqstatic2.PNG" width = "340"></img></div> </div> --- class: center, top # Old Tampa Bay trends <div id="htmlwidget-eda08b72b0656ee00ed2" style="width:100%;height:78%;" class="plotly 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margin: auto;" /> --- class: center, top # Conclusions from last time ## Long-term trends * Overall, nutrients have decreased and seagrasses have recovered ## Concerning recent changes * Recent increases in chlorophyll, increases in diatom density * Temperature increase and salinity decrease in the past ten years * HAB increases in some locations, possibly linked to temperature and salinity, also maybe linked to methodology changes --- class: center, top # Questions for today ## Role of hydrology * Chlorophyll is linked to many factors, nutrients are first! * Hydrology may be a confounding factor driving trends (e.g., compliance load adjustment factors) ## Seasonal differences * Previously evaluated annual trends, as in the NMC action plan * Seasonal differences are also important, i.e., when are exceedances happening and what's driving them? --- class: center, top # Hydrology and nutrient loads <img src="chltrends_files/figure-html/unnamed-chunk-4-1.png" width="100%" style="display: block; margin: auto;" /> --- class: center, top # Salinity (hydrology surrogate) vs chlorophyll <img src="chltrends_files/figure-html/unnamed-chunk-5-1.png" width="100%" style="display: block; margin: auto;" /> --- class: center, top # Explore alternative methods * Use of Weighted Regression (WRTDS) to evaluate past trends ([Hirsch et al. 2010](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307614/), [Beck and Hagy 2015](https://link.springer.com/article/10.1007/s10666-015-9452-8)) * Modelling chlorophyll as a function of time, discharge (flow), and season `$$\Large \ln\left(Chl\right) = \beta_0 + \beta_1 time + \beta_2 Salinity + \beta_3 \sin\left(2\pi \cdot time\right) + \beta_4 \cos\left(2\pi\cdot time \right)$$` -- * Ability to extract "flow-normalized" trend to remove hydrologic influence --- class: center, top # WRTDS method .panelset[ .panel[.panel-name[time] <img src="figure/wrtds_pieces1.PNG" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[salinity] <img src="figure/wrtds_pieces2.PNG" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[season] <img src="figure/wrtds_pieces3.PNG" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[time + salinity] <img src="figure/wrtds_pieces4.PNG" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[time + salinity + season] <img src="figure/wrtds_pieces5.PNG" width="100%" style="display: block; margin: auto;" /> ] ] --- class: center, top # Better predictions relative to time and flow <img src="chltrends_files/figure-html/wrtds_prds-1.png" width="100%" style="display: block; margin: auto;" /> --- class: center, top # Identify flow-normalized trends, annual averages <img src="chltrends_files/figure-html/wrtds_nrms2-1.png" width="100%" style="display: block; margin: auto;" /> --- class: center, top # Identify flow-normalized trends, complete data <img src="chltrends_files/figure-html/wrtds_nrms1-1.png" width="100%" style="display: block; margin: auto;" /> --- class: middle, center # How much of the trend can we explain with hydrology? --- .panelset[ .panel[.panel-name[OTB predictions and hydrology] <img src="chltrends_files/figure-html/unnamed-chunk-13-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[OTB residuals vs anomalies] <img src="chltrends_files/figure-html/unnamed-chunk-14-1.png" width="100%" style="display: block; margin: auto;" /> ] ] --- ## A simple regression model for anomalies .pull-left[ <img src="chltrends_files/figure-html/annreg-1.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ ### Since 2000, hydrology explains 46% of the annual variation in chlorophyll anomalies in OTB <table style="border-collapse:collapse; border:none;"> <tr> <th style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; text-align:left; ">&nbsp;</th> <th colspan="3" style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; ">Chl anomalies</th> </tr> <tr> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; text-align:left; ">Predictors</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">Estimates</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">CI</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">p</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">(Intercept)</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.04</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.27&nbsp;&ndash;&nbsp;0.18</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.684</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">Hydro</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00&nbsp;&ndash;&nbsp;0.00</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; "><strong>0.001</strong></td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm; border-top:1px solid;">Observations</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left; border-top:1px solid;" colspan="3">20</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm;">R² / R² adjusted</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left;" colspan="3">0.460 / 0.430</td> </tr> </table> ] --- class: middle, center # But there is seasonal variation... --- class: top, center # OTB chlorophyll by season .panelset[ .panel[.panel-name[2015] <img src="chltrends_files/figure-html/unnamed-chunk-17-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[2017] <img src="chltrends_files/figure-html/unnamed-chunk-18-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[2019] <img src="chltrends_files/figure-html/unnamed-chunk-19-1.png" width="100%" style="display: block; margin: auto;" /> ] ] --- .panelset[ .panel[.panel-name[OTB predictions and hydrology] <img src="chltrends_files/figure-html/unnamed-chunk-21-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[OTB residuals vs anomalies] <img src="chltrends_files/figure-html/unnamed-chunk-22-1.png" width="100%" style="display: block; margin: auto;" /> ] ] --- class: middle, center # Same plots but arranged by quarter... --- .panelset[ .panel[.panel-name[OTB predictions and hydrology] <img src="chltrends_files/figure-html/unnamed-chunk-23-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[OTB residuals vs anomalies] <img src="chltrends_files/figure-html/unnamed-chunk-24-1.png" width="100%" style="display: block; margin: auto;" /> ] ] --- .panelset[ .panel[.panel-name[JFM] .pull-left[ <img src="chltrends_files/figure-html/jfmreg-1.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ ### Since 2000, hydrology explains 22% of the JFM variation in chlorophyll anomalies in OTB <table style="border-collapse:collapse; border:none;"> <tr> <th style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; text-align:left; ">&nbsp;</th> <th colspan="3" style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; ">Chl anomalies</th> </tr> <tr> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; text-align:left; ">Predictors</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">Estimates</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">CI</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">p</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">(Intercept)</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.08</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.26&nbsp;&ndash;&nbsp;0.10</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.375</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">Hydro</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.01</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00&nbsp;&ndash;&nbsp;0.01</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; "><strong>0.037</strong></td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm; border-top:1px solid;">Observations</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left; border-top:1px solid;" colspan="3">20</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm;">R² / R² adjusted</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left;" colspan="3">0.221 / 0.177</td> </tr> </table> ] ] .panel[.panel-name[AMJ] .pull-left[ <img src="chltrends_files/figure-html/amjreg-1.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ ### Since 2000, hydrology explains 30% of the AMJ variation in chlorophyll anomalies in OTB <table style="border-collapse:collapse; border:none;"> <tr> <th style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; text-align:left; ">&nbsp;</th> <th colspan="3" style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; ">Chl anomalies</th> </tr> <tr> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; text-align:left; ">Predictors</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">Estimates</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">CI</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">p</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">(Intercept)</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.16</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.30&nbsp;&ndash;&nbsp;-0.02</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; "><strong>0.031</strong></td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">Hydro</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00&nbsp;&ndash;&nbsp;0.01</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; "><strong>0.012</strong></td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm; border-top:1px solid;">Observations</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left; border-top:1px solid;" colspan="3">20</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm;">R² / R² adjusted</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left;" colspan="3">0.301 / 0.262</td> </tr> </table> ] ] .panel[.panel-name[JAS] .pull-left[ <img src="chltrends_files/figure-html/jasreg-1.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ ### Since 2000, hydrology explains 48% of the JAS variation in chlorophyll anomalies in OTB <table style="border-collapse:collapse; border:none;"> <tr> <th style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; text-align:left; ">&nbsp;</th> <th colspan="3" style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; ">Chl anomalies</th> </tr> <tr> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; text-align:left; ">Predictors</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">Estimates</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">CI</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">p</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">(Intercept)</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.61</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.24&nbsp;&ndash;&nbsp;1.46</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.151</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">Hydro</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.02</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.01&nbsp;&ndash;&nbsp;0.02</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; "><strong>0.001</strong></td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm; border-top:1px solid;">Observations</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left; border-top:1px solid;" colspan="3">20</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm;">R² / R² adjusted</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left;" colspan="3">0.482 / 0.453</td> </tr> </table> ] ] .panel[.panel-name[OND] .pull-left[ <img src="chltrends_files/figure-html/ondreg-1.png" width="100%" style="display: block; margin: auto;" /> ] .pull-right[ ### Since 2000, hydrology explains 0% of the OND variation in chlorophyll anomalies in OTB <table style="border-collapse:collapse; border:none;"> <tr> <th style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; text-align:left; ">&nbsp;</th> <th colspan="3" style="border-top: double; text-align:center; font-style:normal; font-weight:bold; padding:0.2cm; ">Chl anomalies</th> </tr> <tr> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; text-align:left; ">Predictors</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">Estimates</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">CI</td> <td style=" text-align:center; border-bottom:1px solid; font-style:italic; font-weight:normal; ">p</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">(Intercept)</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.16</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.47&nbsp;&ndash;&nbsp;0.80</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.594</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; ">Hydro</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.00</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">-0.01&nbsp;&ndash;&nbsp;0.02</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:center; ">0.783</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm; border-top:1px solid;">Observations</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left; border-top:1px solid;" colspan="3">20</td> </tr> <tr> <td style=" padding:0.2cm; text-align:left; vertical-align:top; text-align:left; padding-top:0.1cm; padding-bottom:0.1cm;">R² / R² adjusted</td> <td style=" padding:0.2cm; text-align:left; vertical-align:top; padding-top:0.1cm; padding-bottom:0.1cm; text-align:left;" colspan="3">0.004 / -0.051</td> </tr> </table> ] ] ] --- class: middle, center # Another way to look at it... --- class: top, center # OTB salinity prediction surface from WRTDS .panelset[ .panel[.panel-name[All months] <img src="chltrends_files/figure-html/unnamed-chunk-30-1.png" width="100%" style="display: block; margin: auto;" /> ] .panel[.panel-name[Wet season] <img src="chltrends_files/figure-html/unnamed-chunk-31-1.png" width="100%" style="display: block; margin: auto;" /> ] ] --- class: top, center # Conclusions * Chlorophyll is "high" at some places, at some times, and under certain conditions -- * Explains 46% of the annual variation in the last twenty years in OTB -- * Variation is better explained by hydrology during the summer months -- * Must vulnerable is OTB, late summer, high flow/rain -- * Analysis assumes link between hydrology, nutrients, chlorophyll... there may be other factors AND association does not equal causation --- class: top, center # What to do about it? * Consider the most vulnerable locations/times/conditions, plan accordingly -- * Are we evaluating climatic variation or extreme events? -- * Mitigation/restoration activities, e.g., bio-remediation, enhanced circulation, SSO prevention, tidal trib inflows, etc. -- * Follow-up analyses - what is specific role of hydrology with Pyro? Do spring time storms trigger bloom events? Can we link any of these changes to [seagrass](https://tbep-tech.github.io/tbeptools/articles/seagrasstransect.html)? --- class: top, left # Resources .small[ * Hirsch et al. 2010. Weighted regressions on time, discharge, and season (WRTDS), with an application to Chesapeake Bay river inputs. JAWRA, 46(5):857–880. [10.1111/j.1752-1688.2010.00482.x](https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1752-1688.2010.00482.x) * Beck and Hagy, 2015. Adaptation of a weighted regression approach to evaluate water quality trends in an estuary. Env. Mod. Assess. 20:637-655. [10.1007/s10666-015-9452-8](https://link.springer.com/article/10.1007/s10666-015-9452-8) * Beck 2020. WRTDStidal R package. https://github.com/fawda123/WRTDStidal v1.1.3. Zenodo. [10.5281/zenodo.4034843](http://doi.org/10.5281/zenodo.4034843) * Presentation: [link](https://tbep-tech.github.io/tbep-os-presentations/chltrends.html), [source](https://github.com/tbep-tech/tbep-os-presentations/blob/master/chltrends.Rmd) ]