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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Open source reporting tools for the PEP Monitoring Collaborative: Beach Pathogens and Dissolved Oxygen</title>
<meta charset="utf-8" />
<meta name="author" content="Dr. Marcus Beck \bullet @fawda123 \bullet #TampaBayOpensci" />
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<textarea id="source">
class: center, middle, inverse, title-slide
# Open source reporting tools for the PEP Monitoring Collaborative: Beach Pathogens and Dissolved Oxygen
### <a href="mailto:[email protected]">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>
### Peconic Estuary WQ Monitoring Collaborative, Tampa Bay Estuary Program
### 1/29/2021
---
class: left, top
.center[
## AGENDA FOR TODAY
]
1. Brief review of PEP reporting tools: `peptools` R package
1. Development of beach pathogen reporting
1. Development of dissolved oxygen reporting
---
class: left, top
.center[
## GOALS FOR TODAY
]
1. Vibe check: do we like these approaches?
1. Discuss decision points on pathogen reporting
1. Discuss decision points on dissolved oxygen reporting
---
class: center, top
## `peptools` R PACKAGE
<img src="figure/pepintro.PNG" width="100%" style="display: block; margin: auto;" />
.footnote[[https://tbep-tech.github.io/peptools/](https://tbep-tech.github.io/peptools/)]
---
class: center, top
## `peptools` R PACKAGE
<img src="figure/pepfuncs2.png" width="90%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## PAST DECISIONS
]
* Consider existing LTM datasets that can be used to assess progress in attaining CCMP goals (*Goal: Clean Waters*)
--
* Spatial divisions of Peconic Estuary for applying numeric thresholds
--
* Relevant thresholds and how to quantify (median vs. mean)
--
* Stoplight graphic for public-facing documents, update annually
---
class: left, top
.center[
## IT'S SUPER SIMPLE...
]
```r
library(peptools)
dat <- read_pepwq('data/currentdata.xlsx')
show_thrpep(dat, bay_segment = "Western", param = "chla")
```
<img src="peptools2_files/figure-html/unnamed-chunk-4-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## ESTIMATE SEGMENT MEDIANS
]
* All segment annual values based on medians, account for censored data (secchi on bottom)
```r
medpep <- anlz_medpep(dat)
medpep$ann
```
```
## # A tibble: 792 x 5
## bay_segment yr val est var
## <fct> <dbl> <dbl> <chr> <chr>
## 1 Western 2019 3.03 lwr.ci chla
## 2 Western 2019 4.22 medv chla
## 3 Western 2019 6.26 upr.ci chla
## 4 Western 2018 3.89 lwr.ci chla
## 5 Western 2018 4.82 medv chla
## 6 Western 2018 6 upr.ci chla
## 7 Western 2017 3.58 lwr.ci chla
## 8 Western 2017 5.29 medv chla
## 9 Western 2017 7.04 upr.ci chla
## 10 Western 2016 3.14 lwr.ci chla
## # ... with 782 more rows
```
---
.center[
## REPORTING
]
* Provisional targets ([Suffolk Co 2019 SWP](https://suffolkcountyny.gov/Departments/Health-Services/Environmental-Quality#SubWWPlan)) for water clarity and secchi depth
```r
peptargets
```
```
## # A tibble: 3 x 4
## bay_segment name sd_thresh chla_thresh
## <fct> <chr> <dbl> <dbl>
## 1 Western Western 6.5 5.5
## 2 Central Central 6.5 5.5
## 3 Eastern Eastern 6.5 5.5
```
---
.center[
## REPORTING
]
* Apply targets to annual medians
```r
anlz_attainpep(medpep)
```
```
## # A tibble: 132 x 4
## bay_segment yr chla_sd outcome
## <fct> <dbl> <chr> <chr>
## 1 Western 2019 2_3 red
## 2 Western 2018 2_3 red
## 3 Western 2017 2_3 red
## 4 Western 2016 0_3 yellow
## 5 Western 2015 0_2 yellow
## 6 Western 2014 0_0 green
## 7 Western 2013 1_1 yellow
## 8 Western 2012 1_2 yellow
## 9 Western 2011 1_2 yellow
## 10 Western 2010 3_3 red
## # ... with 122 more rows
```
---
class: left, top
.center[
## REPORTING
]
* Annual categories depend on both a __duration__ and __magnitude__ of exceedance
* Jointly considers chlorophyll and water clarity endpoints
--
<img src="figure/outints.png" width="90%" style="display: block; margin: auto;" />
.center[
.footnote[[TBEP tech report #04-00](https://drive.google.com/file/d/1juhfptqA4R-Bq_XfW6nOhqFxJSorGkfq/view?usp=drivesdk)]
]
---
class: left, top
.center[
## REPORTING
]
* Annual categories depend on both a __duration__ and __magnitude__ of exceedance
* Jointly considers chlorophyll and water clarity endpoints
<img src="figure/matrixcats.png" width="80%" style="display: block; margin: auto;" />
.center[
.footnote[[TBEP tech report #04-00](https://drive.google.com/file/d/1juhfptqA4R-Bq_XfW6nOhqFxJSorGkfq/view?usp=drivesdk)]
]
---
class: left, top
.center[
## REPORTING
]
* Translate segment water quality conditions into annual reporting categories to inform/prioritize management actions towards CCMP goals
--
* In Tampa...
<span style="color:#33FF3B; text-shadow: 0 0 3px #333;">__Stay the Course__</span>: Continue planned projects. Report data via annual progress reports and Baywide Environmental Monitoring Report.
<span style="color:#F9FF33; text-shadow: 0 0 3px #333;">__Caution__</span>: Review monitoring data and nitrogen loading estimates. Begin/continue TAC and Management Board development of specific management recommendations.
<span style="color:#FF3333; text-shadow: 0 0 3px #333;">__On Alert__</span>: Finalize development and implement appropriate management actions to get back on track.
---
class: left, top
.center[
## REPORTING
]
```r
show_matrixpep(dat, asreact = TRUE, nrows = 8)
```
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---
class: left, top
.center[
## REPORTING
]
```r
show_plotlypep(rawdat, bay_segment = 'Western')
```
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2018<br />medv: 4.0500<br />colour: Annual Median","yr: 2019<br />medv: 3.9800<br />colour: Annual Median"],"type":"scatter","mode":"markers+lines","marker":{"autocolorscale":false,"color":"rgba(255,0,0,1)","opacity":1,"size":11.3385826771654,"symbol":"circle","line":{"width":1.88976377952756,"color":"rgba(255,0,0,1)"}},"hoveron":"points","name":"Annual Median","legendgroup":"Annual Median","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","line":{"width":2.83464566929134,"color":"rgba(255,0,0,1)","dash":"solid"},"frame":null},{"x":[1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019],"y":[4.1,4.75,3.65,3.55,2.975,5.4,5.76666666666667,6.26,3.28,3.1,2.345,2.9588,2.9432,4.2224,3.6712,3.9962,4.0768,3.8324,3.9988,4.524,6.4974,3.9312,4.0404,4.77,2.825,2.395,3.28,4.46,4.26,4.08],"text":["yr: 1990<br />lwr.ci: 3.5000<br />upr.ci: 4.700000<br />colour: Annual Median","yr: 1991<br 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Median","legendgroup":"Annual Median","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[1989.445,2019.555],"y":[5.5,5.5],"text":"thrnum: 5.5<br />colour: Threshold","type":"scatter","mode":"lines","line":{"width":2.83464566929134,"color":"rgba(0,0,255,1)","dash":"dot"},"hoveron":"points","name":"Threshold","legendgroup":"Threshold","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[2018.5,2019.5,2019.5,2018.5,2018.5,null,2017.5,2018.5,2018.5,2017.5,2017.5],"y":[2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5],"text":"Result: 0, Exceedance: none (size), NA (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2012.5,2013.5,2013.5,2012.5,2012.5,null,2011.5,2012.5,2012.5,2011.5,2011.5,null,2010.5,2011.5,2011.5,2010.5,2010.5,null,2004.5,2005.5,2005.5,2004.5,2004.5,null,2003.5,2004.5,2004.5,2003.5,2003.5,null,2002.5,2003.5,2003.5,2002.5,2002.5,null,2001.5,2002.5,2002.5,2001.5,2001.5,null,2000.5,2001.5,2001.5,2000.5,2000.5,null,1999.5,2000.5,2000.5,1999.5,1999.5,null,1998.5,1999.5,1999.5,1998.5,1998.5,null,1997.5,1998.5,1998.5,1997.5,1997.5,null,1990.5,1991.5,1991.5,1990.5,1990.5,null,1989.5,1990.5,1990.5,1989.5,1989.5],"y":[2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5],"text":"Result: 0, Exceedance: none (size), none (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2015.5,2016.5,2016.5,2015.5,2015.5,null,2014.5,2015.5,2015.5,2014.5,2014.5,null,2013.5,2014.5,2014.5,2013.5,2013.5,null,2007.5,2008.5,2008.5,2007.5,2007.5,null,2006.5,2007.5,2007.5,2006.5,2006.5,null,2005.5,2006.5,2006.5,2005.5,2005.5,null,1993.5,1994.5,1994.5,1993.5,1993.5,null,1992.5,1993.5,1993.5,1992.5,1992.5,null,1991.5,1992.5,1992.5,1991.5,1991.5,null,2013.5,2014.5,2014.5,2013.5,2013.5],"y":[2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 0, Exceedance: none (size), short (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2008.5,2009.5,2009.5,2008.5,2008.5,null,1994.5,1995.5,1995.5,1994.5,1994.5,null,2012.5,2013.5,2013.5,2012.5,2012.5],"y":[2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 1, Exceedance: small (size), short (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2006.5,2007.5,2007.5,2006.5,2006.5,null,2005.5,2006.5,2006.5,2005.5,2005.5,null,1997.5,1998.5,1998.5,1997.5,1997.5],"y":[0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 2, Exceedance: small (size), long (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2016.5,2017.5,2017.5,2016.5,2016.5],"y":[2.5,2.5,3.5,3.5,2.5],"text":"Result: 2, Exceedance: small (size), NA (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2013.5,2014.5,2014.5,2013.5,2013.5],"y":[1.5,1.5,2.5,2.5,1.5],"text":"Result: Stay the Course (chla: 0, sd: 0)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(0,255,0,1)","hoveron":"fills","name":"green","legendgroup":"green","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2009.5,2010.5,2010.5,2009.5,2009.5,null,1995.5,1996.5,1996.5,1995.5,1995.5],"y":[2.5,2.5,3.5,3.5,2.5,null,2.5,2.5,3.5,3.5,2.5],"text":"Result: 1, Exceedance: small (size), short (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[1996.5,1997.5,1997.5,1996.5,1996.5,null,2011.5,2012.5,2012.5,2011.5,2011.5,null,2010.5,2011.5,2011.5,2010.5,2010.5],"y":[2.5,2.5,3.5,3.5,2.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 2, Exceedance: large (size), short (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2014.5,2015.5,2015.5,2014.5,2014.5,null,2003.5,2004.5,2004.5,2003.5,2003.5,null,2001.5,2002.5,2002.5,2001.5,2001.5,null,2000.5,2001.5,2001.5,2000.5,2000.5,null,1998.5,1999.5,1999.5,1998.5,1998.5,null,1993.5,1994.5,1994.5,1993.5,1993.5],"y":[0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 2, Exceedance: small (size), long (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2018.5,2019.5,2019.5,2018.5,2018.5],"y":[0.5,0.5,1.5,1.5,0.5],"text":"Result: 2, Exceedance: small (size), NA (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2015.5,2016.5,2016.5,2015.5,2015.5,null,2009.5,2010.5,2010.5,2009.5,2009.5,null,2008.5,2009.5,2009.5,2008.5,2008.5,null,2007.5,2008.5,2008.5,2007.5,2007.5,null,2004.5,2005.5,2005.5,2004.5,2004.5,null,2002.5,2003.5,2003.5,2002.5,2002.5,null,1999.5,2000.5,2000.5,1999.5,1999.5,null,1996.5,1997.5,1997.5,1996.5,1996.5,null,1995.5,1996.5,1996.5,1995.5,1995.5,null,1994.5,1995.5,1995.5,1994.5,1994.5,null,1992.5,1993.5,1993.5,1992.5,1992.5,null,1991.5,1992.5,1992.5,1991.5,1991.5,null,1990.5,1991.5,1991.5,1990.5,1990.5,null,1989.5,1990.5,1990.5,1989.5,1989.5],"y":[0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 3, Exceedance: large (size), long (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2017.5,2018.5,2018.5,2017.5,2017.5,null,2016.5,2017.5,2017.5,2016.5,2016.5],"y":[0.5,0.5,1.5,1.5,0.5,null,0.5,0.5,1.5,1.5,0.5],"text":"Result: 3, Exceedance: large (size), NA (length)","type":"scatter","mode":"lines","line":{"width":0.377952755905512,"color":"rgba(0,0,0,1)","dash":"solid"},"fill":"toself","fillcolor":"rgba(255,0,0,1)","hoveron":"fills","name":"red","legendgroup":"red","showlegend":false,"xaxis":"x","yaxis":"y2","hoverinfo":"text","frame":null},{"x":[2009.5,2010.5,2010.5,2009.5,2009.5,null,2008.5,2009.5,2009.5,2008.5,2008.5,null,1995.5,1996.5,1996.5,1995.5,1995.5,null,1994.5,1995.5,1995.5,1994.5,1994.5],"y":[1.5,1.5,2.5,2.5,1.5,null,1.5,1.5,2.5,2.5,1.5,null,1.5,1.5,2.5,2.5,1.5,null,1.5,1.5,2.5,2.5,1.5],"text":"Result: On Alert (chla: 1, sd: 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---
class: left, top
.center[
## BEACH PATHOGENS
]
* 28 swimming/bathing beaches in the Peconic Estuary
--
* *Enterococcus* concentrations monitored by SCDHS
--
* Beaches are closed if concentrations are high
--
* Data can be summarized to understand __relative risk__ of exposure
--
.center[
.footnote[[https://tbep-tech.github.io/peptools/articles/pathogens.html](https://tbep-tech.github.io/peptools/articles/pathogens.html)]
]
---
class: left, top
.center[
## PATHOGENS: IMPORT
]
* Data are available as a spreadsheet [here](https://gisportal.suffolkcountyny.gov/gis/home/item.html?id=025cb4dadb57413980dbd7e760b94da8)
<img src="figure/enteroraw.PNG" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## PATHOGENS: IMPORT
]
* Import the data with [`read_pepent()`](https://tbep-tech.github.io/peptools/reference/read_pepent.html)
```r
path <- system.file('extdata', 'enterodata.xlsx',
package = 'peptools')
entdat <- read_pepent(path)
head(entdat)
```
```
## # A tibble: 6 x 5
## Name FieldNum Date value status
## <chr> <chr> <dttm> <dbl> <chr>
## 1 Alberts Landing Beach EH7 2010-06-29 09:47:00 4 "<"
## 2 Alberts Landing Beach EH7 2010-07-27 09:49:00 4 "<"
## 3 Alberts Landing Beach EH7 2010-08-13 09:18:00 28 ""
## 4 Alberts Landing Beach EH7 2011-06-22 10:21:00 4 "<"
## 5 Alberts Landing Beach EH7 2011-07-20 10:57:00 4 "<"
## 6 Alberts Landing Beach EH7 2011-08-17 11:14:00 4 "<"
```
---
class: left, top
.center[
## PATHOGENS: SUMMARIZE
]
* Summarize the data with [`anlz_entpep()`](https://tbep-tech.github.io/peptools/reference/anlz_entpep.html)
* This creates a count of exceedances in each 24 hour period for each year and each beach
--
```r
entsum <- anlz_entpep(entdat)
head(entsum)
```
```
## # A tibble: 6 x 5
## Name yr samples exceedances proexceedances
## <chr> <dbl> <int> <int> <dbl>
## 1 Alberts Landing Beach 2010 3 0 0
## 2 Alberts Landing Beach 2011 3 0 0
## 3 Alberts Landing Beach 2012 4 0 0
## 4 Alberts Landing Beach 2013 3 0 0
## 5 Alberts Landing Beach 2014 4 0 0
## 6 Alberts Landing Beach 2015 3 0 0
```
---
class: left, top
.center[
## PATHOGENS: PLOT
]
* Plot the results with [`show_entmatrix()`](https://tbep-tech.github.io/peptools/reference/show_entmatrix.html)
```r
show_entmatrix(entdat)
```
<img src="peptools2_files/figure-html/unnamed-chunk-15-1.png" width="100%" height="60%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## PATHOGENS: DISCUSS
]
* This plot communicates exposure risk, NOT beach closures
--
* Exceedances based on concentrations above 104 cfu/100 mL
--
* We can change this...
---
class: left, top
.center[
## PATHOGENS: DISCUSS
]
* Changing the default arguments...
```r
show_entmatrix(entdat, thr = 35)
```
<img src="peptools2_files/figure-html/unnamed-chunk-16-1.png" width="100%" height="60%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## DISSOLVED OXYGEN
]
* Two continuous USGS monitoring stations in Peconic Estuary
--
* Peconic River (01304562) and Orient Harbor (01304200)
--
* Data can be summarized to understand hypoxia frequency/duration
--
.center[
.footnote[[https://tbep-tech.github.io/peptools/articles/dissolvedoxygen.html](https://tbep-tech.github.io/peptools/articles/dissolvedoxygen.html)]
]
---
class: left, top
.center[
## DO: IMPORT
]
* Data can be downloaded directly from USGS data source with [`read_pepdo()`](https://tbep-tech.github.io/peptools/reference/read_pepdo.html)
```r
exdat <- read_pepdo(site = c('01304562', '01304200'),
nms = c('Peconic R.', 'Orient Harbor'),
startDate = '2013-01-01', endDate = '2020-06-30')
head(exdat)
```
```
## site DateTime do_mgl
## 1 Orient Harbor 2013-01-01 00:00:00 11.2
## 2 Orient Harbor 2013-01-01 00:06:00 11.2
## 3 Orient Harbor 2013-01-01 00:12:00 11.2
## 4 Orient Harbor 2013-01-01 00:18:00 11.2
## 5 Orient Harbor 2013-01-01 00:24:00 11.2
## 6 Orient Harbor 2013-01-01 00:30:00 11.2
```
---
class: left, top
.center[
## DO: IMPORT
]
<img src="peptools2_files/figure-html/unnamed-chunk-19-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## DO: IMPORT
]
<img src="peptools2_files/figure-html/unnamed-chunk-20-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## CHALLENGES WITH DO DATA
]
* DO data have diurnal and seasonal variation, how can we summarize this to quantify hypoxia stress?
--
* Hypoxia can have both acute and chronic impacts, how can we summarize the DO data to express magnitude and duration of hypoxia?
---
class: left, top
.center[
## DO: SUMMARIZE
]
* Summarize the data with [`anlz_domopep()`](https://tbep-tech.github.io/peptools/reference/anlz_domopep.html)
--
* Gets the following for each month:
* Mean daily DO
* Proportion of days with low DO (magnitude)
* Max run of days with low DO (duration)
---
class: left, top
.center[
## DO: SUMMARIZE
]
* Summarize the data with [`anlz_domopep()`](https://tbep-tech.github.io/peptools/reference/anlz_domopep.html)
```r
anlz_domopep(dodat, thr = 3)
```
```
## # A tibble: 189 x 6
## site yr mo do_mgl below_ave below_maxrun
## * <fct> <dbl> <ord> <dbl> <dbl> <dbl>
## 1 Peconic River 2013 Jan 11.6 0 0
## 2 Peconic River 2013 Feb 11.9 0 0
## 3 Peconic River 2013 Mar 11.7 0 0
## 4 Peconic River 2013 Apr 9.55 0 0
## 5 Peconic River 2013 May 7.90 0 0
## 6 Peconic River 2013 Jun 5.73 0.3 5
## 7 Peconic River 2013 Jul 3.12 1 27
## 8 Peconic River 2013 Aug 3.13 1 24
## 9 Peconic River 2013 Sep 4.81 0.655 6
## 10 Peconic River 2013 Oct 6.03 0.348 7
## # ... with 179 more rows
```
---
class: left, top
.center[
## DO: PLOT
]
* Plot the results with [`show_domatrix()`](https://tbep-tech.github.io/peptools/reference/show_domatrix.html)
```r
show_domatrix(dodat, thr = 3, show = 'below_ave')
```
<img src="peptools2_files/figure-html/unnamed-chunk-22-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## DO: PLOT
]
* Plot the results with [`show_domatrix()`](https://tbep-tech.github.io/peptools/reference/show_domatrix.html)
```r
show_domatrix(dodat, thr = 3, show = 'below_maxrun')
```
<img src="peptools2_files/figure-html/unnamed-chunk-23-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## DO: PLOT
]
* Plot the results with [`show_domatrix()`](https://tbep-tech.github.io/peptools/reference/show_domatrix.html)
```r
show_domatrix(dodat, thr = 4.8, show = 'below_ave')
```
<img src="peptools2_files/figure-html/unnamed-chunk-24-1.png" width="100%" style="display: block; margin: auto;" />
---
class: left, top
.center[
## DO: DISCUSS
]
* The summaries show relative hypoxia stress between locations, with stress quantified as magnitude or duration
--
* What is the relevance of the threshold to a meaningful endpoint?
--
* Are there breakpoints we need to consider?
--
* What can we reasonably say about the spatial extent of hypoxia?
---
class: left, top
.center[
## RESOURCES
]
* Pathogens vignette: [link](https://tbep-tech.github.io/peptools/articles/pathogens.html)
* Dissolved oxygen vignette: [link](https://tbep-tech.github.io/peptools/articles/dissolvedoxygen.html)
* Package overview vignette: [link](https://tbep-tech.github.io/peptools/articles/Introduction.html)
* `peptools` package website: [link](https://tbep-tech.github.io/peptools/)
* `peptools` GitHub source: [link](https://github.com/tbep-tech/peptools)
---
class: left, top
.center[
## GOALS FOR TODAY
]
1. Vibe check: do we like these approaches?
1. Discuss decision points on pathogen reporting
1. Discuss decision points on dissolved oxygen reporting
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