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Background

Fecal Indicator Bacteria (FIB) are used to track concentrations of pathogens in surface waters that may be detrimental to human health and the environment. Exposure risk is commonly measured with select indicators that are present in the human gut and can enter the environment through wastewater discharges, stormwater, or other illicit sources. Common indicators include concentrations of E. coli, Enterococcus, or Fecal Coliform as the number of colony forming units (CFU) per 100 mL of water.

Many monitoring programs routinely measure FIB concentrations at select locations. The tbeptools package has several functions for importing and reporting these data. Three workflows are available:

  1. Functions that use data exclusively from the Environmental Protection Commission (EPC) of Hillsborough County
  2. Functions that use data exclusively from Manatee County Natural Resources Department
  3. Functions that use data from several monitoring programs for baywide reporting focusing exclusively on Enterococcus

This vignette is organized around these three workflows. For all, the assessments are meant to inform progress remediating fecal impairments or to support prioritization of areas for further investigation. They are not meant to support beach monitoring efforts or closures for recreational uses - alternative reporting products are available for that purpose (see FLDOH Healthy Beaches).

EPC reporting

The Environmental Protection Commission (EPC) of Hillsborough County has been tracking FIB indicators for several decades as part of their long-term monitoring. Functions in tbeptools can be used to download EPC FIB data, analyze the results, and create summary maps or plots. This sections describes use of these functions. Most of these functions are focused on reporting for the Hillsborough River fecal coliform impairment and the associated Basin Management Action Plan (BMAP). These tools can be used to track long-term changes in FIBs in this basin to assess progress in reducing fecal coliform levels.

Data collected from the monitoring program are processed and maintained in a spreadsheet titled RWMDataSpreadsheet_ThroughCurrentReportMonth.xlsx available for direct download here and viewable here. These data include observations at all stations and for all parameters throughout the period of record. FIB data are collected at most stations where additional water quality data are collected. This is the same dataset used for reporting on water quality indicators in Tampa Bay (see the water quality data vignette). The functions in tbeptools can be used to import and analyze these data.

Read

The main function for importing FIB data is read_importfib(). This function downloads the latest file if one is not already available at the location specified by the xlsx input argument. The function operates similarly as read_importwq() for importing water quality data. Please refer to the water quality data vignette for additional details on the import function.

The FIB data can be downloaded as follows:

fibdata <- read_importfib('vignettes/current_data.xlsx', download_latest = T)

A data object called fibdata is also provided with the package, although it may not contain the most current data available from EPC. View the help file for the download date.

fibdata
#> # A tibble: 77,526 × 18
#>    area   epchc_station class SampleTime             yr    mo Latitude Longitude
#>    <chr>          <dbl> <chr> <dttm>              <dbl> <dbl>    <dbl>     <dbl>
#>  1 Hills…             2 3M    2024-06-10 14:51:00  2024     6     27.9     -82.5
#>  2 Hills…             6 3M    2024-06-17 09:25:00  2024     6     27.9     -82.5
#>  3 Hills…             7 3M    2024-06-17 09:42:00  2024     6     27.9     -82.5
#>  4 Hills…             8 3M    2024-06-17 12:39:00  2024     6     27.9     -82.4
#>  5 Middl…             9 2     2024-06-17 11:47:00  2024     6     27.8     -82.4
#>  6 Middl…            11 2     2024-06-17 10:04:00  2024     6     27.8     -82.5
#>  7 Middl…            13 2     2024-06-17 10:18:00  2024     6     27.8     -82.5
#>  8 Middl…            14 2     2024-06-17 11:14:00  2024     6     27.8     -82.5
#>  9 Middl…            16 2     2024-06-25 09:37:00  2024     6     27.7     -82.5
#> 10 Middl…            19 2     2024-06-25 09:52:00  2024     6     27.7     -82.6
#> # ℹ 77,516 more rows
#> # ℹ 10 more variables: Total_Depth_m <dbl>, Sample_Depth_m <dbl>, ecoli <dbl>,
#> #   ecoli_q <chr>, entero <dbl>, entero_q <chr>, fcolif <dbl>, fcolif_q <chr>,
#> #   totcol <dbl>, totcol_q <chr>

The fibdata object includes monthly samples for FIB data at select stations in the Hillsborough River basin. Some stations include samples beginning in 1972. The default output for read_importfib() returns all stations with FIB data from EPC. If all = F for read_importfib(), only stations with AreaName as Hillsborough River, Hillsborough River Tributary, Alafia River, Alafia River Tributary, Lake Thonotosassa, Lake Thonotosassa Tributary, and Lake Roberta are returned. Values are returned for E. coli (ecoli), Enterococcus (entero), Fecal Coliform (fcolif), and Total Coliform (totcol). Units are # of colonies per 100 mL of water (#/100mL). Qualifier columns for each are also returned with the _q suffix. Consult the source spreadsheet for interpretation of these codes. Concentrations noted with < (below detection) or > (above detection) in the raw data are reported as the detection limit.

The fibdata object can be used for the remaining FIB functions.

Analyze

Several analysis functions are provided for working with the EPC data. These functions are used internally by the show functions described below, but are presented here for an explanation of how the data are processed.

The anlz_fibmap() function assigns categories to each observation in fibdata for a selected month and year. These results are then mapped using anlz_fibmap() (see below). The categories are specific to E. coli or Enterococcus and are assigned based on the station class as freshwater (class as 1 or 3F) or marine (class as 2 or 3M), respectively. A station is categorized into one of four ranges defined by the thresholds as noted in the cat column of the output, with corresponding colors appropriate for each range as noted in the col column of the output.

anlz_fibmap(fibdata)
#> # A tibble: 77,526 × 12
#>    area    station class    yr    mo Latitude Longitude ecoli entero ind   cat  
#>    <chr>     <dbl> <chr> <dbl> <dbl>    <dbl>     <dbl> <dbl>  <dbl> <chr> <fct>
#>  1 Hillsb…       2 3M     2024     6     27.9     -82.5    NA      3 Ente… < 35 
#>  2 Hillsb…       6 3M     2024     6     27.9     -82.5    NA      8 Ente… < 35 
#>  3 Hillsb…       7 3M     2024     6     27.9     -82.5    NA      2 Ente… < 35 
#>  4 Hillsb…       8 3M     2024     6     27.9     -82.4    NA      4 Ente… < 35 
#>  5 Middle…       9 2      2024     6     27.8     -82.4    NA      2 Ente… < 35 
#>  6 Middle…      11 2      2024     6     27.8     -82.5    NA      2 Ente… < 35 
#>  7 Middle…      13 2      2024     6     27.8     -82.5    NA      2 Ente… < 35 
#>  8 Middle…      14 2      2024     6     27.8     -82.5    NA      2 Ente… < 35 
#>  9 Middle…      16 2      2024     6     27.7     -82.5    NA      4 Ente… < 35 
#> 10 Middle…      19 2      2024     6     27.7     -82.6    NA      2 Ente… < 35 
#> # ℹ 77,516 more rows
#> # ℹ 1 more variable: col <chr>

The ranges (number of samples / 100 mL) are from EPC and are as follows for E. coli or Enterococcus.

Indicator Color Range
E. coli Green < 126
Yellow 126 - 409
Orange 410 - 999
Red > 999
Enterococcus Green < 35
Yellow 35 - 129
Orange 130 - 999
Red > 999

The yrsel and mosel arguments can be used to filter results by year and month. Not specifying these arguments will return results for the entire period of record.

anlz_fibmap(fibdata, yrsel = 2023, mosel = 7)
#> # A tibble: 207 × 12
#>    area    station class    yr    mo Latitude Longitude ecoli entero ind   cat  
#>    <chr>     <dbl> <chr> <dbl> <dbl>    <dbl>     <dbl> <dbl>  <dbl> <chr> <fct>
#>  1 Hillsb…       2 3M     2023     7     27.9     -82.5    NA    800 Ente… 130 …
#>  2 Hillsb…       6 3M     2023     7     27.9     -82.5    NA      2 Ente… < 35 
#>  3 Hillsb…       7 3M     2023     7     27.9     -82.5    NA      2 Ente… < 35 
#>  4 Hillsb…       8 3M     2023     7     27.9     -82.4    NA      2 Ente… < 35 
#>  5 Middle…       9 2      2023     7     27.8     -82.4    NA      2 Ente… < 35 
#>  6 Middle…      11 2      2023     7     27.8     -82.5    NA      2 Ente… < 35 
#>  7 Middle…      13 2      2023     7     27.8     -82.5    NA      2 Ente… < 35 
#>  8 Middle…      14 2      2023     7     27.8     -82.5    NA      2 Ente… < 35 
#>  9 Middle…      16 2      2023     7     27.7     -82.5    NA      2 Ente… < 35 
#> 10 Middle…      19 2      2023     7     27.7     -82.6    NA      2 Ente… < 35 
#> # ℹ 197 more rows
#> # ℹ 1 more variable: col <chr>

The areasel argument can indicate either "Alafia" or "Hillsborough" to select data for the corresponding river basins, where rows in fibdata are filtered based on the selection. All stations are returned if this argument is NULL (default). The Alafia River basin includes values in the area column of fibdata as "Alafia River" and "Alafia River Tributary". The Hillsborough River basin includes values in the area column of fibdata as "Hillsborough River", "Hillsborough River Tributary", "Lake Thonotosassa", "Lake Thonotosassa Tributary", and "Lake Roberta". Not all areas may be present based on the selection for yrsel and mosel. All valid options for areasel include "Alafia River", "Hillsborough River", "Big Bend", "Cockroach Bay", "East Lake Outfall", "Hillsborough Bay", "Little Manatee", "Lower Tampa Bay", "McKay Bay", "Middle Tampa Bay", "Old Tampa Bay", "Palm River", "Tampa Bypass Canal", or "Valrico Lake".

anlz_fibmap(fibdata, yrsel = 2023, mosel = 7, areasel = 'Hillsborough River')
#> # A tibble: 47 × 12
#>    area    station class    yr    mo Latitude Longitude ecoli entero ind   cat  
#>    <chr>     <dbl> <chr> <dbl> <dbl>    <dbl>     <dbl> <dbl>  <dbl> <chr> <fct>
#>  1 Hillsb…       2 3M     2023     7     27.9     -82.5    NA    800 Ente… 130 …
#>  2 Hillsb…     105 3M     2023     7     28.0     -82.4    NA    128 Ente… 35 -…
#>  3 Hillsb…     106 1      2023     7     28.1     -82.4   144    232 E. c… 126 …
#>  4 Lake T…     107 3F     2023     7     28.0     -82.3   570   1550 E. c… 410 …
#>  5 Hillsb…     108 3F     2023     7     28.1     -82.2   187    276 E. c… 126 …
#>  6 Lake T…     118 3F     2023     7     28.1     -82.3     4      7 E. c… < 126
#>  7 Hillsb…     120 3F     2023     7     28.1     -82.4   100    410 E. c… < 126
#>  8 Lake T…     135 3F     2023     7     28.1     -82.3     4      4 E. c… < 126
#>  9 Hillsb…     137 3M     2023     7     28.0     -82.5    NA    680 Ente… 130 …
#> 10 Hillsb…     143 3F     2023     7     28.1     -82.1   800   1333 E. c… 410 …
#> # ℹ 37 more rows
#> # ℹ 1 more variable: col <chr>

The anlz_fibmatrix() function creates a summary of FIB categories by station and year as output for the show_fibmatrix() function described below. The function assigns Microbial Water Quality Assessment (MWQA) letter categories for each station and year based on the likelihood that fecal coliform concentrations will exceed 400 CFU / 100 mL. By default, the results for each year are based on a right-centered window that uses the previous two years and the current year to calculate probabilities from the monthly samples (lagyr = 3). The columns for each station and year include the estimated geometric mean of fecal coliform concentrations (gmean) and a category indicating a letter outcome based on the likelihood of exceedences (cat). The indic argument must be set explicitly as 'fcolif' to indicate the indicator as fecal coliform for the EPC data.

anlz_fibmatrix(fibdata, indic = 'fcolif')
#> # A tibble: 459 × 6
#>       yr grp   gmean Latitude Longitude cat  
#>    <dbl> <fct> <dbl>    <dbl>     <dbl> <chr>
#>  1  1974 143      NA       NA        NA NA   
#>  2  1974 108      NA       NA        NA NA   
#>  3  1974 107      NA       NA        NA NA   
#>  4  1974 135      NA       NA        NA NA   
#>  5  1974 118      NA       NA        NA NA   
#>  6  1974 148      NA       NA        NA NA   
#>  7  1974 105      NA       NA        NA NA   
#>  8  1974 152      NA       NA        NA NA   
#>  9  1974 137      NA       NA        NA NA   
#> 10  1975 143      NA       NA        NA NA   
#> # ℹ 449 more rows

Show

The show_fibmap() function creates a map of FIB sites and thresholds based on output from anlz_fibmap(). The same arguments that apply to anlz_fibmap() also apply to show_fibmap() such that freshwater and marine stations categorized by relevant thresholds are plotted by a selected year, month, and area. Unlike anlz_fibmap(), the yrsel and mosel arguments are required.

show_fibmap(fibdata, yrsel = 2023, mosel = 7, areasel = NULL)

Sites for the Hillsborough or Alafia river basins can be shown using the areasel argument.

show_fibmap(fibdata, yrsel = 2023, mosel = 7, areasel = 'Hillsborough River')
show_fibmap(fibdata, yrsel = 2023, mosel = 7, areasel = 'Alafia River')

Additional information about a site can be seen by placing the cursor over a location. A map inset can also be seen by clicking the arrow on the bottom left of the map.

The show_fibmatrix() function creates a stoplight graphic of summarized FIB data at selected stations for each year of available data [1]. The matrix colors are based on the likelihood that fecal indicator bacteria concentrations exceed 400 CFU / 100 mL (using Fecal Coliform, fcolif in fibdata). The likelihoods are categorized as A, B, C, D, or E (Microbial Water Quality Assessment or MWQA categories) with corresponding colors, where the breakpoints for each category are <10%, 10-30%, 30-50%, 50-75%, and >75% (right-closed). Methods and rationale for this categorization scheme are provided by the Florida Department of Environmental Protection, Figure 8 in [2] and [1].

By default, the results for each year are based on a right-centered window that uses the previous two years and the current year to calculate probabilities from the monthly samples (lagyr = 3). This example shows results using only the monthly observations in each year.

show_fibmatrix(fibdata, lagyr = 1)

The default stations are those used in TBEP report #05-13 [3] for the Hillsborough River Basin Management Action Plan (BMAP) subbasins. These include Blackwater Creek (WBID 1482, EPC stations 143, 108), Baker Creek (WBID 1522C, EPC station 107), Lake Thonotosassa (WBID 1522B, EPC stations 135, 118), Flint Creek (WBID 1522A, EPC station 148), and the Lower Hillsborough River (WBID 1443E, EPC stations 105, 152, 137). Other stations in fibdata can be plotted using the stas argument.

show_fibmatrix(fibdata, stas = c(115, 116))

The yrrng argument can also be used to select a year range, where the default is 1985 to the most current year of data in fibdata.

show_fibmatrix(fibdata, yrrng = c(1990, 2020))

If preferred, the matrix can also be returned in an HTML table that can be sorted and scrolled. Only the first ten rows are shown by default. The default number of rows (10) can be changed with the nrows argument. Use a sufficiently large number to show all rows.

show_fibmatrix(fibdata, asreact = TRUE)

A plotly (interactive, dynamic plot) object can be returned by setting the plotly argument to TRUE.

show_fibmatrix(fibdata, plotly = TRUE)

Finally, a map of station categories for a given year can be plotted using show_fibmatrixmap(). The yrsel argument is required, and the areasel argument can be used to select a specific area. The values shown on the map are the same as those for the respective year in the show_fibmatrix() function.

show_fibmatmap(fibdata, indic = 'fcolif', yrsel = 2020, areasel = c('Hillsborough River', 'Alafia River'))

Manatee County reporting

FIB data from the Manatee County Natural Resources Department can also be used with the above functions. These data can be downloaded as follows:

mancofibdata <- read_importwqp('21FLMANA_WQX', type = 'fib')

For convenience, a data object with same name as the above is included with tbeptools for use with all FIB functions. Note that read_importwqp() can be used to download FIB data from other organizations, although the FIB functions will only work with data from Manatee County.

Similar workflows as for the EPCHC data can be used. Examples of the functions using Manatee County data:

show_fibmap(mancofibdata, yrsel = 2023, mosel = 7, areasel = NULL)
show_fibmatrix(mancofibdata, plotly = TRUE)
show_fibmatmap(mancofibdata, yrsel = 2020, indic = 'fcolif', areasel = 'Manatee River')

Baywide reporting

The second workflow uses a baywide approach to summarize FIB data. Select stations were identified at downstream locations that drain into Tampa Bay and considered important watershed endpoints for FIB monitoring. Enterococcus is the primary indicator because these stations are located at terminal downstream locations that are tidally influenced. The functions are organized similarly as the EPC reporting workflow, with some unique functions for working with data from these locations and other functions repeated from the EPC workflow that differ in the output depending on the data inputs.

Read

The main function for importing Enterococcus data is read_importentero(). This function retrieves data from the USEPA water quality portal using their API. The three arguments are stas, startDate, and endDate. The stas argument can be left as NULL (default) to retrieve data from all stations based on those in the catchprecip data object, described below. The startDate and endDate arguments specify the date ranges for retrieving data, where the input format for each is a character string as 'YYYY-MM-DD'.

read_importentero(startDate = '1995-01-01', endDate = '2023-12-31')

The data request can take some time and the enterodata data object is provided with the package for use with all downstream functions. This dataset includes all data from the 53 selected stations from 1995-2023.

head(enterodata)
#>            date   yr mo time time_zone     long_name bay_segment
#> 1901 2001-01-16 2001  1                Old Tampa Bay         OTB
#> 1902 2001-02-20 2001  2                Old Tampa Bay         OTB
#> 1903 2001-03-20 2001  3                Old Tampa Bay         OTB
#> 1904 2001-04-17 2001  4                Old Tampa Bay         OTB
#> 1905 2001-05-15 2001  5                Old Tampa Bay         OTB
#> 1906 2001-06-19 2001  6                Old Tampa Bay         OTB
#>               station entero entero_censored MDL entero_units qualifier
#> 1901 21FLHILL_WQX-101     80           FALSE  NA      #/100mL        NA
#> 1902 21FLHILL_WQX-101    360           FALSE  NA      #/100mL        NA
#> 1903 21FLHILL_WQX-101   3900           FALSE  NA      #/100mL        NA
#> 1904 21FLHILL_WQX-101     20           FALSE  NA      #/100mL        NA
#> 1905 21FLHILL_WQX-101     NA           FALSE  20                     NA
#> 1906 21FLHILL_WQX-101     NA           FALSE  20                     NA
#>      LabComments Latitude Longitude
#> 1901          NA  28.0248  -82.6316
#> 1902          NA  28.0248  -82.6316
#> 1903          NA  28.0248  -82.6316
#> 1904          NA  28.0248  -82.6316
#> 1905          NA  28.0248  -82.6316
#> 1906          NA  28.0248  -82.6316

The downstream functions also require precipitation data obtained using the read_importrain() function. This function downloads daily precipitation data from the Southwest Florida Water Management District (SWFWMD) rainfall FTP website. For each station, daily cumulative rainfall is summarized for each upstream catchment, where the catchments for each site are defined by pixel locations used to describe the SWFWMD rainfall data. This information is available in the catchpixels data object.

Rainfall data is downloaded by defining years and months of interest.

read_importrain(2021, catchpixels, mos = 1:12, quiet = F)

As for the enterodata data object, the catchprecip object is provided with the package for use with all downstream functions. This dataset includes daily rainfall data (inches) for the 53 selected stations from 1995-2023. The rainfall data is used to define Enterococcus samples as “wet” or “dry” based on default or user-defined thresholds described below.

head(catchprecip)
#> # A tibble: 6 × 3
#>   station            date        rain
#>   <chr>              <date>     <dbl>
#> 1 21FLCOSP_WQX-32-03 1995-01-01 0    
#> 2 21FLCOSP_WQX-32-03 1995-01-02 0    
#> 3 21FLCOSP_WQX-32-03 1995-01-03 0    
#> 4 21FLCOSP_WQX-32-03 1995-01-04 0.389
#> 5 21FLCOSP_WQX-32-03 1995-01-05 0    
#> 6 21FLCOSP_WQX-32-03 1995-01-06 0.106

Analyze

Several analysis functions are provided for working with Enterococcus data. These functions are used internally by the show functions described below, but are presented here for an explanation of how the data are processed.

Each function uses Enterococcus and precipitation data provided by the enterodata and catchprecip data objects. The latter dataset is used to define “wet” or “dry” samples with the premise that Enterococcus concentrations are higher in wet weather and it may be useful to distinguish these samples to assess progress in achieving water quality restoration goals, i.e., rainfall may confound an assessment of management efforts to reduce fecal contamination.

Each anlz function has optional arguments that define the temporal_window and wet_threshold for defining “wet” or “dry” samples, which are passed to the anlz_fibwetdry() function. These arguments define a period of time preceding a sample date and cumulative rainfall threshold within the time period that must be met to define a sample as “wet”. These arguments default to two days and half an inch, such that samples are defined as “wet” if they have greater than half an inch of cumulative rainfall in the two days preceding and including the sample date. The time and rainfall thresholds can be changed by the user. Additionally, the anlz functions can also treat all samples equally by ignoring any rainfall data by setting wetdry = FALSE, which is the default behavior.

The anlz_fibwetdry() function defines “wet” or “dry” samples as described above and returns the original input dataset with three additional columns describing the total rain (inches) on the day of sampling (rain_sampleDay), the total rain in the period defined by the temporal_window argument (rain_total), and whether the sample is “wet” or not as a logical value (wet_sample).

anlz_fibwetdry(enterodata, catchprecip, temporal_window = 2, wet_threshold = 0.5)
#> # A tibble: 6,266 × 19
#>    date          yr    mo time  time_zone long_name   bay_segment station entero
#>    <date>     <dbl> <dbl> <chr> <chr>     <chr>       <chr>       <chr>    <dbl>
#>  1 2001-01-16  2001     1 ""    ""        Old Tampa … OTB         21FLHI…     80
#>  2 2001-02-20  2001     2 ""    ""        Old Tampa … OTB         21FLHI…    360
#>  3 2001-03-20  2001     3 ""    ""        Old Tampa … OTB         21FLHI…   3900
#>  4 2001-04-17  2001     4 ""    ""        Old Tampa … OTB         21FLHI…     20
#>  5 2001-05-15  2001     5 ""    ""        Old Tampa … OTB         21FLHI…     NA
#>  6 2001-06-19  2001     6 ""    ""        Old Tampa … OTB         21FLHI…     NA
#>  7 2001-07-24  2001     7 ""    ""        Old Tampa … OTB         21FLHI…   1300
#>  8 2001-08-21  2001     8 ""    ""        Old Tampa … OTB         21FLHI…    260
#>  9 2001-09-18  2001     9 ""    ""        Old Tampa … OTB         21FLHI…    420
#> 10 2001-10-16  2001    10 ""    ""        Old Tampa … OTB         21FLHI…    520
#> # ℹ 6,256 more rows
#> # ℹ 10 more variables: entero_censored <lgl>, MDL <int>, entero_units <chr>,
#> #   qualifier <lgl>, LabComments <lgl>, Latitude <dbl>, Longitude <dbl>,
#> #   rain_sampleDay <dbl>, rain_total <dbl>, wet_sample <lgl>

The remaining anlz functions are anlz_enteromap() to prepare data for mapping and anlz_fibmatrix() to prepare data for a score card. Both can optionally use anlz_fibwetdry() to plot “wet” or “dry” samples, described further in the show section.

The anlz_enteromap() function is an Enterococcus-specific analogue to the anlz_fibmap() fecal coliform function described in the EPC section above. The function assigns categories to each observation in the Enterococcus data frame, which can be viewed for a given month and year using show_enteromap() (analagous to show_fibmap()). The categories are specific to Enterococcus in marine waters, and are noted in the cat column of the output. Corresponding colors are in the col column of the output.

anlz_enteromap(enterodata)
#> # A tibble: 6,266 × 12
#>    station     long_name    yr    mo Latitude Longitude entero cat   col   ind  
#>    <chr>       <chr>     <dbl> <dbl>    <dbl>     <dbl>  <dbl> <fct> <chr> <chr>
#>  1 21FLHILL_W… Old Tamp…  2001     1     28.0     -82.6     80 35 -… #E9C… Ente…
#>  2 21FLHILL_W… Old Tamp…  2001     2     28.0     -82.6    360 130 … #EE7… Ente…
#>  3 21FLHILL_W… Old Tamp…  2001     3     28.0     -82.6   3900 > 999 #CC3… Ente…
#>  4 21FLHILL_W… Old Tamp…  2001     4     28.0     -82.6     20 < 35  #2DC… Ente…
#>  5 21FLHILL_W… Old Tamp…  2001     5     28.0     -82.6     NA NA    NA    Ente…
#>  6 21FLHILL_W… Old Tamp…  2001     6     28.0     -82.6     NA NA    NA    Ente…
#>  7 21FLHILL_W… Old Tamp…  2001     7     28.0     -82.6   1300 > 999 #CC3… Ente…
#>  8 21FLHILL_W… Old Tamp…  2001     8     28.0     -82.6    260 130 … #EE7… Ente…
#>  9 21FLHILL_W… Old Tamp…  2001     9     28.0     -82.6    420 130 … #EE7… Ente…
#> 10 21FLHILL_W… Old Tamp…  2001    10     28.0     -82.6    520 130 … #EE7… Ente…
#> # ℹ 6,256 more rows
#> # ℹ 2 more variables: indnm <chr>, conc <dbl>

The ranges (number of samples / 100 mL) are from EPC and are as follows for Enterococcus:

Color Range
Green < 35
Yellow 35 - 129
Red > 999
Orange 130 - 999

The yrsel and mosel arguments can be used to filter results by year and month. Not specifying these arguments will return results for the entire period of record.

anlz_enteromap(enterodata, yrsel = 2020, mosel = 8)
#> # A tibble: 27 × 12
#>    station     long_name    yr    mo Latitude Longitude entero cat   col   ind  
#>    <chr>       <chr>     <dbl> <dbl>    <dbl>     <dbl>  <dbl> <fct> <chr> <chr>
#>  1 21FLHILL_W… Old Tamp…  2020     8     28.0     -82.6    220 130 … #EE7… Ente…
#>  2 21FLHILL_W… Old Tamp…  2020     8     28.0     -82.6     40 35 -… #E9C… Ente…
#>  3 21FLHILL_W… Old Tamp…  2020     8     28.0     -82.6     70 35 -… #E9C… Ente…
#>  4 21FLHILL_W… Old Tamp…  2020     8     28.0     -82.6     50 35 -… #E9C… Ente…
#>  5 21FLPDEM_W… Old Tamp…  2020     8     27.9     -82.7     20 < 35  #2DC… Ente…
#>  6 21FLHILL_W… Hillsbor…  2020     8     27.9     -82.4      8 < 35  #2DC… Ente…
#>  7 21FLHILL_W… Hillsbor…  2020     8     27.9     -82.4   1200 > 999 #CC3… Ente…
#>  8 21FLHILL_W… Hillsbor…  2020     8     27.8     -82.4    520 130 … #EE7… Ente…
#>  9 21FLHILL_W… Hillsbor…  2020     8     27.9     -82.5    190 130 … #EE7… Ente…
#> 10 21FLHILL_W… Hillsbor…  2020     8     27.9     -82.4     90 35 -… #E9C… Ente…
#> # ℹ 17 more rows
#> # ℹ 2 more variables: indnm <chr>, conc <dbl>

The wetdry argument can be used to determine whether a sample was taken after a rain event (logical wet_sample column in output), based on user-specified thresholds and a provided precipitation data object (catchprecip). Below shows how to identify wet samples based on at least 0.5 inches of rain occurring two days prior to and including the sample date.

anlz_enteromap(enterodata, wetdry = TRUE, precipdata = catchprecip,
               temporal_window = 2, wet_threshold = 0.5)
#> # A tibble: 6,266 × 13
#>    station     long_name    yr    mo Latitude Longitude entero cat   col   ind  
#>    <chr>       <chr>     <dbl> <dbl>    <dbl>     <dbl>  <dbl> <fct> <chr> <chr>
#>  1 21FLHILL_W… Old Tamp…  2001     1     28.0     -82.6     80 35 -… #E9C… Ente…
#>  2 21FLHILL_W… Old Tamp…  2001     2     28.0     -82.6    360 130 … #EE7… Ente…
#>  3 21FLHILL_W… Old Tamp…  2001     3     28.0     -82.6   3900 > 999 #CC3… Ente…
#>  4 21FLHILL_W… Old Tamp…  2001     4     28.0     -82.6     20 < 35  #2DC… Ente…
#>  5 21FLHILL_W… Old Tamp…  2001     5     28.0     -82.6     NA NA    NA    Ente…
#>  6 21FLHILL_W… Old Tamp…  2001     6     28.0     -82.6     NA NA    NA    Ente…
#>  7 21FLHILL_W… Old Tamp…  2001     7     28.0     -82.6   1300 > 999 #CC3… Ente…
#>  8 21FLHILL_W… Old Tamp…  2001     8     28.0     -82.6    260 130 … #EE7… Ente…
#>  9 21FLHILL_W… Old Tamp…  2001     9     28.0     -82.6    420 130 … #EE7… Ente…
#> 10 21FLHILL_W… Old Tamp…  2001    10     28.0     -82.6    520 130 … #EE7… Ente…
#> # ℹ 6,256 more rows
#> # ℹ 3 more variables: indnm <chr>, conc <dbl>, wet_sample <lgl>

The areasel argument can indicate one or any of the major subwatersheds in Tampa Bay (excluding Terra Ceia Bay where no data exist). For example, use Old Tampa Bay for stations in the subwatershed of Old Tampa Bay, where rows in enterodata are filtered based on the selection. All stations are returned if this argument is set as NULL (default). All valid options for areasel include "Old Tampa Bay", "Hillsborough Bay", "Middle Tampa Bay", "Lower Tampa Bay", "Boca Ciega Bay", or "Manatee River".

anlz_enteromap(enterodata, yrsel = 2023, mosel = 7, areasel = 'Old Tampa Bay')
#> # A tibble: 12 × 12
#>    station     long_name    yr    mo Latitude Longitude entero cat   col   ind  
#>    <chr>       <chr>     <dbl> <dbl>    <dbl>     <dbl>  <dbl> <fct> <chr> <chr>
#>  1 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6      5 < 35  #2DC… Ente…
#>  2 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6     30 < 35  #2DC… Ente…
#>  3 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6     70 35 -… #E9C… Ente…
#>  4 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6    220 130 … #EE7… Ente…
#>  5 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.5     NA NA    NA    Ente…
#>  6 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6    467 130 … #EE7… Ente…
#>  7 21FLHILL_W… Old Tamp…  2023     7     28.0     -82.6   3900 > 999 #CC3… Ente…
#>  8 21FLPDEM_W… Old Tamp…  2023     7     28.0     -82.7    798 130 … #EE7… Ente…
#>  9 21FLPDEM_W… Old Tamp…  2023     7     27.9     -82.7    457 130 … #EE7… Ente…
#> 10 21FLPDEM_W… Old Tamp…  2023     7     27.9     -82.7   1860 > 999 #CC3… Ente…
#> 11 21FLPDEM_W… Old Tamp…  2023     7     27.9     -82.7     75 35 -… #E9C… Ente…
#> 12 21FLTPA_WQ… Old Tamp…  2023     7     28.0     -82.7   2613 > 999 #CC3… Ente…
#> # ℹ 2 more variables: indnm <chr>, conc <dbl>

The anlz_fibmatrix() function is used with the show_fibmatrix() function and is used similarly as for the EPC workflow described above. The function assigns Microbial Water Quality Assessment (MWQA) letter categories for each station and year based on the likelihood that Enterococcus concentrations will exceed 130 CFU / 100 mL. By default, the results for each year are based on a right-centered window that uses the previous two years and the current year to calculate probabilities from the monthly samples (lagyr = 3). The columns for each station and year include the estimated geometric mean of fecal coliform concentrations (gmean) and a category indicating a letter outcome based on the likelihood of exceedences (cat). The indic argument must be set explicitly as 'entero' to select the indicator as Enterococcus.

anlz_fibmatrix(enterodata, indic = 'entero')
#> # A tibble: 1,176 × 6
#>       yr grp                        gmean Latitude Longitude cat  
#>    <dbl> <fct>                      <dbl>    <dbl>     <dbl> <chr>
#>  1  2000 21FLCOSP_WQX-32-03            NA       NA        NA NA   
#>  2  2000 21FLCOSP_WQX-44-02            NA       NA        NA NA   
#>  3  2000 21FLCOSP_WQX-48-03            NA       NA        NA NA   
#>  4  2000 21FLCOSP_WQX-CENTRAL CANAL    NA       NA        NA NA   
#>  5  2000 21FLCOSP_WQX-COSP580          NA       NA        NA NA   
#>  6  2000 21FLCOSP_WQX-NORTH CANAL      NA       NA        NA NA   
#>  7  2000 21FLCOSP_WQX-SC-01            NA       NA        NA NA   
#>  8  2000 21FLCOSP_WQX-SOUTH CANAL      NA       NA        NA NA   
#>  9  2000 21FLDOH_WQX-MANATEE152        NA       NA        NA NA   
#> 10  2000 21FLHILL_WQX-101              NA       NA        NA NA   
#> # ℹ 1,166 more rows

Show

The show_enteromap() function creates a map of Enterococcus sites and thresholds based on output from anlz_enteromap(). The same arguments that apply to anlz_enteromap() also apply to show_enteromap(), including classification of samples as ‘wet’ or not depending on specified thresholds. Wet and dry samples are differentiated on the map by their shapes. Unlike anlz_enteromap(), the yrsel and mosel arguments are required.

show_enteromap(enterodata, yrsel = 2020, mosel = 9)
show_enteromap(enterodata, yrsel = 2020, mosel = 9, wetdry = TRUE,
               temporal_window = 2, wet_threshold = 0.5)

Additional information about a site can be seen by placing the cursor over a location. A map inset can also be seen by clicking the arrow on the bottom left of the map.

Sites for specific areas can be shown using the areasel argument.

show_enteromap(enterodata, yrsel = 2023, mosel = 7, areasel = 'Old Tampa Bay')

The show_fibmatrix() function creates a stoplight graphic of summarized FIB data at selected stations for each year of available data. The function was primarily designed for fecal coliform data, but has been adapted to work with Enterococcus data. The matrix color codes years and stations based on the likelihood of fecal indicator bacteria concentrations exceeding 130 CFU / 100 mL for Enterococcus (entero in both fibdata and enterodata). The likelihoods are categorized as A, B, C, D, or E (Microbial Water Quality Assessment or MWQA categories) with corresponding colors, where the breakpoints for each category are <10%, 10-30%, 30-50%, 50-75%, and >75% (right-closed). Methods and rationale for this categorization scheme are provided by the Florida Department of Environmental Protection, Figure 8 in [2] and [1]. All stations are shown by default.

show_fibmatrix(enterodata, indic = 'entero')

By default, the results for each year are based on a right-centered window that uses the previous two years and the current year to calculate probabilities from the monthly samples (lagyr = 3). This example shows results using only the monthly observations in each year.

show_fibmatrix(enterodata, indic = 'entero', lagyr = 1)

Individual stations can be selectd using the stas argument.

show_fibmatrix(enterodata,
               indic = 'entero',
               stas = c('21FLHILL_WQX-101', '21FLHILL_WQX-102', '21FLHILL_WQX-103'))

The yrrng argument can also be used to select a year range, where the default is the date range contained in the data.

show_fibmatrix(enterodata, indic = 'entero', yrrng = c(2015, 2020))

Note that the subset_wetdry argument can be used with show_fibmatrix() to show only wet or dry samples based on the thresholds provided by temporal_window and wet_threshold. However, this is not recommended because the scores are probability-based and comparisons between wet or dry samples may be misleading due to different sample sizes, and therefore, power to detect the likelihood of exceeding the threshold. Specifically, there are far fewer wet samples than dry and these samples will generally receive higher grades due to lower power of the statistical tests.

As for the EPC data, an HTML table can be returned with show_fibmatrix() using asreact = TRUE and a plotly object can be returned using plotly = TRUE. See the above section for examples of these outputs.

The show_fibmatrix() function also supports baywide reporting by bay segment, unlike the EPC data. The stations for the baywide reporting were selected specifically as endpoints that drain directly into each bay segment and an aggregate summary of the stations by bay segment can indicate the MWQA category. The calculations are the same as by station, but the data are aggregated by bay segment.

show_fibmatrix(enterodata, indic = 'entero', bay_segment = c('OTB', 'HB', 'MTB', 'LTB', 'BCB', 'MR'))

Finally, a map of station and bay segment categories for a given year can be plotted using show_fibmatrixmap(). The yrsel argument is required, and the areasel argument can be used to select a specific area. The values shown on the map are the same as those for the respective year in the show_fibmatrix() function.

show_fibmatmap(enterodata, indic = 'entero', yrsel = 2020, areasel = c('OTB', 'HB', 'MTB', 'LTB', 'BCB', 'MR'))

Retrieving additional FIB data

The read_importwqp() function can be used to retrieve data from the USEPA Water Quality Portal using an organization identifier. The data can be retrieved as follows and will typically take less than one minute to download.

# get Manatee County data
mancodata <- read_importwqp(org = '21FLMANA_WQX', type = 'fib', trace = T)

# get Pinellas County data
pincodata <- read_importwqp(org = '21FLPDEM_WQX', type = 'fib', trace = T)

References

[1]
G. Morrison, H. N. Swanson, V. J. Harwood, C. M. Wapnick, T. Hansen, H. S. Greening, Using a ’Decision Matrix’ Approach to Develop a Fecal Coliform BMAP for Impaired Waters in the Hillsborough River Watershed, Tampa Bay Estuary Program, Tampa Bay Regional Planning Council, St. Petersburg, Florida, 2009.
[2]
PBS & J, Terra Ceia Consulting, LLC, University of South Florida, Development of a decision-support tool to support the implementation of fecal coliform BMAPs in the Hillsborough River Watershed, Florida Department of Environmental Protection, Jacksonville, Florida, 2008. http://publicfiles.dep.state.fl.us/DEAR/BMAP/Tampa/MST%20Report/Fecal%20BMAP%20DST%20Final%20Report%20--%20June%202008.pdf.
[3]
E. Sherwood, G. Morrison, Hillsborough River Fecal Coliform BMAP Update (2013), Tampa Bay Estuary Program, St. Petersburg, Florida, 2013. https://drive.google.com/file/d/1MZnK3cMzV7LRg6dTbCKX8AOZU0GNurJJ/view?usp=drivesdk.