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fixing some typos
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@fawda123
fawda123 committed Feb 6, 2020
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32 changes: 16 additions & 16 deletions wq-dash.Rmd
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Expand Up @@ -155,7 +155,7 @@ otbclkrct <- reactive({
out <- selfun(selin, boxplototb, algdat, epcdata, 'OTB')
validate(
need(nrow(out) > 0, 'No phtyoplankton data')
need(nrow(out) > 0, 'No phytoplankton data')
)
return(out)
Expand Down Expand Up @@ -197,7 +197,7 @@ hbclkrct <- reactive({
out <- selfun(selin, boxplothb, algdat, epcdata, 'HB')
validate(
need(nrow(out) > 0, 'No phtyoplankton data')
need(nrow(out) > 0, 'No phytoplankton data')
)
return(out)
Expand Down Expand Up @@ -239,7 +239,7 @@ mtbclkrct <- reactive({
out <- selfun(selin, boxplotmtb, algdat, epcdata, 'MTB')
validate(
need(nrow(out) > 0, 'No phtyoplankton data')
need(nrow(out) > 0, 'No phytoplankton data')
)
return(out)
Expand Down Expand Up @@ -281,7 +281,7 @@ ltbclkrct <- reactive({
out <- selfun(selin, boxplotltb, algdat, epcdata, 'LTB')
validate(
need(nrow(out) > 0, 'No phtyoplankton data')
need(nrow(out) > 0, 'No phytoplankton data')
)
return(out)
Expand Down Expand Up @@ -667,7 +667,7 @@ Column {data-width=650}

### WELCOME TO THE TAMPA BAY WATER QUALITY REPORT CARD!

#### Backround
#### Background

Light availability to seagrass is the guiding paradigm for TBEP’s Nitrogen Management Strategy. Because excessive nitrogen loads to the bay generally lead to increased algae blooms (higher chlorophyll-a levels) and reduce light penetration to seagrass, an evaluation method was developed to assess whether load reduction strategies are achieving desired water quality results (i.e. reduced chlorophyll-a concentrations and increased water clarity).

Expand All @@ -680,7 +680,7 @@ knitr::include_graphics('www/nitro.PNG')
The different tabs on the dashboard can be used to view the long-term trends in water quality for each bay segment and individual monitoring stations.

1) __ATTAINMENT MATRICES__: This tab shows the overall report card for the bay as management action categories described above. Separate matrices for chlorophyll and light attenuation exceedances (as a "large" magnitude) for major bay segments are also shown. An interactive map is provided that shows attainment outcomes by year for individual stations in the bay. Note that the map shows site-specific attainments for bay segment targets as a reference only.
1) __SEGMENT ANNUAL TRENDS__: This tab shows time series of chlorophyll and light attenuation averages for each bay segment. Blue lines on each plot show management targets or thresholds that define exceedance categories used to create the management action categories. In between the chlorophyll and light attenation plots show the attainment matrix outcomes that are specific to each segment. The top row in the matrix shows the attainment outcome for chlorophyll, the bottom row shows the attainment outcome for light attenuation, and the middle row shows the overall management attainment outcome that combines information from both the chloropyl and light attenuation outcomes.
1) __SEGMENT ANNUAL TRENDS__: This tab shows time series of chlorophyll and light attenuation averages for each bay segment. Blue lines on each plot show management targets or thresholds that define exceedance categories used to create the management action categories. In between the chlorophyll and light attenuation plots show the attainment matrix outcomes that are specific to each segment. The top row in the matrix shows the attainment outcome for chlorophyll, the bottom row shows the attainment outcome for light attenuation, and the middle row shows the overall management attainment outcome that combines information from both the chlorophyll and light attenuation outcomes.
1) __SEGMENT SEASONAL TRENDS__: This tab shows the seasonal distributions by bay segment for chlorophyll and light attenuation. Each boxplot shows the monthly distribution of observations across all available years in the dataset. The jittered points overlaid on the boxplots show the individual values for a specific year and the large red point shows the current year. Each observation can be clicked to view the observed phytoplankton cell counts for the selected year/month combination.
1) __SITE TRENDS__: This tab shows the time series for chlorophyll and light attenuation at individual stations (as compared to segment averages in the other tabs). Stations can be selected by clicking on the location in the map. Pytoplankton cell counts can also be viewed as quarterly sums across the period of record.

Expand All @@ -702,7 +702,7 @@ The attainment outcomes shown in the various dashboard tabs are built on a rigor

<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.

The management category or action is based on the combination of outcomes for chlorophyll and light attenuation. For each year, major bay segments are assigned to outcome categories based on both the exceedance of the annual estimate above a threshold or target and duration of the exceedance for the years prior. Exceedances are defined as either small or large based on the magnitude and short or long based on the duration within the previous four years. The combination of these exceedance categories creates an outcome integer that each bay segment is assigned for both chlorophyll and light attenutation.
The management category or action is based on the combination of outcomes for chlorophyll and light attenuation. For each year, major bay segments are assigned to outcome categories based on both the exceedance of the annual estimate above a threshold or target and duration of the exceedance for the years prior. Exceedances are defined as either small or large based on the magnitude and short or long based on the duration within the previous four years. The combination of these exceedance categories creates an outcome integer that each bay segment is assigned for both chlorophyll and light attenuation.

```{r out.width='40%', fig.align='center', fig.cap='Outcomes for annual estimates of water quality are assigned an integer value from zero to three depending on both magnitude and duration of the exceedence.'}
knitr::include_graphics('www/outints.png')
Expand Down Expand Up @@ -742,7 +742,7 @@ knitr::include_graphics('www/attainex.PNG')
```
<br>

In the above example, the attainment outcome for Old Tampa Bay in 1980 was <span style="color:#FF3333; text-shadow: 0 0 3px #333;">On Alert</span>. Additional information on chorophyll and light attenuation outcomes that drive the overall attainment outcome are also provided. For Old Tampa Bay in 1980, chlorophyll and light attenuation both received an outcome of "3" (possible integer values ranging from 0 to 3, with three indicating water quality conditions less suitable for seagrass growth). The integer values describe both a magnitude and duration of exceedance for chlorophyll and light attenuation:
In the above example, the attainment outcome for Old Tampa Bay in 1980 was <span style="color:#FF3333; text-shadow: 0 0 3px #333;">On Alert</span>. Additional information on chlorophyll and light attenuation outcomes that drive the overall attainment outcome are also provided. For Old Tampa Bay in 1980, chlorophyll and light attenuation both received an outcome of "3" (possible integer values ranging from 0 to 3, with three indicating water quality conditions less suitable for seagrass growth). The integer values describe both a magnitude and duration of exceedance for chlorophyll and light attenuation:

<br>
```{r out.width='70%', fig.align='center'}
Expand All @@ -758,7 +758,7 @@ knitr::include_graphics('www/matrixcats.png')
```
<br>

Additional tabs show the chlorophyll and light attenuation exceedance outcomes for each year and bay segment. For example, hovering a mouse over the chlorophyll matrix will show the average concentration for the segment and year, whether the value exceeded a "large" magnitude value, and the corresdonding value. In this example, OTB in 1980 had an average chlorophyll concenctration of 13.9 ug/L, which was above the threshold of 9.3 for the bay segment.
Additional tabs show the chlorophyll and light attenuation exceedance outcomes for each year and bay segment. For example, hovering a mouse over the chlorophyll matrix will show the average concentration for the segment and year, whether the value exceeded a "large" magnitude value, and the corresponding value. In this example, OTB in 1980 had an average chlorophyll concentration of 13.9 ug/L, which was above the threshold of 9.3 for the bay segment.

<br>
```{r, out.width='70%', fig.align='center'}
Expand All @@ -768,15 +768,15 @@ knitr::include_graphics('www/chlattainex.PNG')

A similar matrix is provided for light attenuation. It is important to note that in both the chlorophyll and light attenuation matrices, the reference values represent a large exceedance value defined as twice the standard error of the historic average for years when water quality conditions were favorable for seagrass growth.

Finally, an interactive map is provided on the right to demonstrate which stations were above or below water quality targets defined for each bay segment. These targets differ from the large exceedance values in the attainment matrices, where the latter was defined as twice the standard error of the former. The points are color-coded to show if the target was met and sized by the relative concentation or attenuation values observed in the selected year. Hovering the mouse pointer over each station will show the following:
Finally, an interactive map is provided on the right to demonstrate which stations were above or below water quality targets defined for each bay segment. These targets differ from the large exceedance values in the attainment matrices, where the latter was defined as twice the standard error of the former. The points are color-coded to show if the target was met and sized by the relative concentration or attenuation values observed in the selected year. Hovering the mouse pointer over each station will show the following:

<br>
```{r, out.width='70%', fig.align='center'}
knitr::include_graphics('www/targetmapex.PNG')
```
<br>

Results for different years and for chloropyll or light attenuation can be chosen from the drop-down menus.
Results for different years and for chlorophyll or light attenuation can be chosen from the drop-down menus.

### ATTAINMENT MATRIX

Expand Down Expand Up @@ -825,7 +825,7 @@ Column {data-width=275}

This tab shows time series of chlorophyll and light attenuation averages for each bay segment. Blue lines on each plot show management targets or thresholds that define exceedance categories used to create the management action categories (i.e., <span style="color:#33FF3B; text-shadow: 0 0 3px #333;">__Stay the Course__</span>, <span style="color:#F9FF33; text-shadow: 0 0 3px #333;">__Caution__</span>, or <span style="color:#FF3333; text-shadow: 0 0 3px #333;">__On Alert__</span>.

In between the chlorophyll and light attenation plots are the attainment matrix outcomes that are specific to each segment. The top row in the matrix shows the attainment outcome for chlorophyll, the bottom row shows the attainment outcome for light attenuation, and the middle row shows the overall management attainment outcome that combines information from both the chloropyl and light attenuation outcomes. These are the same matrix outcomes as in the __ATTAINMENT MATRICES__ tab, but combined for the selected bay segment.
In between the chlorophyll and light attenuation plots are the attainment matrix outcomes that are specific to each segment. The top row in the matrix shows the attainment outcome for chlorophyll, the bottom row shows the attainment outcome for light attenuation, and the middle row shows the overall management attainment outcome that combines information from both the chlorophyll and light attenuation outcomes. These are the same matrix outcomes as in the __ATTAINMENT MATRICES__ tab, but combined for the selected bay segment.

Understanding the results in the plots can provide context for the overall management outcome shown in the middle row of the center plot. The management outcome is based on patterns of both chlorophyll and light attenuation, magnitude of the observed values, and a temporal component that measures how long exceedances were observed. These outcomes that are assigned to chlorophyll and light attenuation are assigned as follows:

Expand Down Expand Up @@ -857,7 +857,7 @@ knitr::include_graphics('www/otbout3.PNG')
```
<br>

In both cases, the average values for 1980 for chlorohyll and light attenuation had a large magnitude exceedance of long duration, placing the year in the "3" category. The exceedance values are defined by the blue lines in the time series plots and the duration values are defined by how many times the average values were above the management target within the previous four years. A "long" duration means that average values in the previous four years were all above the management target, i.e., the water quality conditions have persisted for some time.
In both cases, the average values for 1980 for chlorophyll and light attenuation had a large magnitude exceedance of long duration, placing the year in the "3" category. The exceedance values are defined by the blue lines in the time series plots and the duration values are defined by how many times the average values were above the management target within the previous four years. A "long" duration means that average values in the previous four years were all above the management target, i.e., the water quality conditions have persisted for some time.

The plots are especially useful to identify which water quality conditions are driving the overall management outcome. Zooming in on 2015 to 2019 for Old Tampa Bay shows that the consistent <span style="color:#F9FF33; text-shadow: 0 0 3px #333;">__Caution__</span> categories are driven by non-sequential years of large magnitude and long duration exceedances for chlorophyll. Light attenuation values have remained below the target.

Expand Down Expand Up @@ -924,9 +924,9 @@ knitr::include_graphics('www/boxplothoverex.PNG')
```
<br>

The above example shows the popup text displayed after hovering over a point in the lower light attenuation plot. The outlier value in July was observed in 1979. Each observation can also be clicked to view the observed phytoplankton cell counts for the selected year/month combination. Once a point is clicked, a stacked barplot of count values is shown on the right if phytoplankton data are available for the selected year, month, and bay segment combination. If data are unavailable, text indicating "No phtyoplankton data" will be displayed where the plot should be. The count data represent sums across segment stations of all observations for different phytoplankon taxa.
The above example shows the popup text displayed after hovering over a point in the lower light attenuation plot. The outlier value in July was observed in 1979. Each observation can also be clicked to view the observed phytoplankton cell counts for the selected year/month combination. Once a point is clicked, a stacked barplot of count values is shown on the right if phytoplankton data are available for the selected year, month, and bay segment combination. If data are unavailable, text indicating "No phytoplankton data" will be displayed where the plot should be. The count data represent sums across segment stations of all observations for different phytoplankton taxa.

Viewing phytoplankton cell count data can be useful to determine if any bloom events may have contributed to conditions that differ from the typical seasonal ranges for a given month. The example below shows counts for July 2019 in Old Tampa Bay. High chlorophyll concentrations were observed in July, which can be explained by blooms of *Pyrodinium bahamanese*.
Viewing phytoplankton cell count data can be useful to determine if any bloom events may have contributed to conditions that differ from the typical seasonal ranges for a given month. The example below shows counts for July 2019 in Old Tampa Bay. High chlorophyll concentrations were observed in July, which can be explained by blooms of *Pyrodinium bahamense*.

<br>
```{r, fig.align='center', out.width='40%'}
Expand Down Expand Up @@ -1033,7 +1033,7 @@ knitr::include_graphics('www/stationsel3.PNG')
```
<br>

The phytoplankton cell counts on the top plot show summed counts for the selected station in quarterly time periods (e.g., Jan/Feb/Mar 2005, Apr/May/Jun 2005, etc.). These plots are useful to undestand variation in dominant phytoplankton taxa over time at a station. The plot can also be filtered to show specific taxa by clicking on the names in the legend. The example below shows trends in *Pyrodinium bahamense* at station 66:
The phytoplankton cell counts on the top plot show summed counts for the selected station in quarterly time periods (e.g., Jan/Feb/Mar 2005, Apr/May/Jun 2005, etc.). These plots are useful to understand variation in dominant phytoplankton taxa over time at a station. The plot can also be filtered to show specific taxa by clicking on the names in the legend. The example below shows trends in *Pyrodinium bahamense* at station 66:

<br>
```{r, fig.align='center', out.width='100%'}
Expand Down

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