Beach Pathogens • peptools

Regular monitoring of swimming beach pathogens is conducted by Suffolk County Department of Health Services (SCDHS). As noted on the Suffolk County website (https://www.suffolkcountyny.gov/Departments/Health-Services/Environmental-Quality/Ecology/Beach-Monitoring-Program), water quality at swimming beaches can be adversely affected by episodic sources such as stormwater runoff, wastewater discharges from boats or land-based septic systems, and fecal material from pets and wildlife. To provide information on the potential presence of pathogens public in swimming areas that may be impacted by such contamination, the Suffolk County Department of Health Services (SCDHS) conducts a comprehensive bathing beach water quality monitoring program from May through September each year. Sampling is performed by SCDHS staff, with analyses conducted by the Department’s accredited Public and Environmental Health Laboratory (PEHL). Data are available here.

Information from this monitoring program can be summarized to communicate the relative risk of exposure to pathogens at bathing beaches in the Peconic Estuary. Functions in the peptools package can be used to import the pathogen data provided by SCHDS and PEHL, analyze relative exceedances of pathogen criterion, and plot the results in an easily interpretable format. This vignette describes use of these functions.

For package installation instructions, please see the Introduction vignette.

Data import and processing

The beaches data object includes 31 beaches that are relevant for assessing pathogen exposure risk for the Peconic Estuary Program.

beaches
#>                                                 Name FieldNum Tier
#> 1                              Alberts Landing Beach      EH7    3
#> 2                                Camp Blue Bay Beach      EH2    2
#> 3                                Camp Quinipet Beach      ST1    3
#> 4                                   Clearwater Beach      EH3    3
#> 5  Cornell Cooperative Extension Marine Center Beach      S25    3
#> 6                           Crescent Beach - Suffolk      ST3    3
#> 7                              Culloden Shores Beach      EH4    3
#> 8                             Devon Yacht Club Beach     EH39    3
#> 9                              East Lake Drive Beach     EH12    3
#> 10                           Fifth Street Park Beach      S12    2
#> 11                                 Fleets Neck Beach      S16    3
#> 12                             Foster Memorial Beach      SH9    3
#> 13                            Founders Landing Beach      S14    2
#> 14                                 Goose Creek Beach      S13    2
#> 15                                      Havens Beach      EH1    2
#> 16                                   Maidstone Beach      EH5    3
#> 17                                    Meschutt Beach      SH5    3
#> 18                       Nassau Point Causeway Beach      S15    3
#> 19                                 New Suffolk Beach      S17    3
#> 20                        Norman E. Klipp Park Beach      S11    3
#> 21                          Perlman Music Camp Beach     ST10    3
#> 22                               Pridwin Hotel Beach      ST2    3
#> 23           Shelter Island Heights Beach Club Beach      ST6    2
#> 24                          Silver Sands Motel Beach      S26    3
#> 25                             South Jamesport Beach      R14    3
#> 26     Southampton Peconic Beach & Tennis Club Beach      SH7    3
#> 27                     Veteran's Memorial Park Beach      S18    3
#> 28                                       Wades Beach      ST4    3
#>               geometry
#> 1  -72.11667, 41.00013
#> 2  -72.17883, 41.03910
#> 3  -72.37873, 41.07053
#> 4  -72.16710, 41.05097
#> 5  -72.38863, 41.03622
#> 6  -72.36563, 41.07412
#> 7  -71.94862, 41.07292
#> 8  -72.10570, 40.99253
#> 9  -71.93562, 41.07820
#> 10 -72.36612, 41.09298
#> 11 -72.46508, 41.00562
#> 12 -72.32688, 40.99640
#> 13 -72.41335, 41.06050
#> 14 -72.41348, 41.05227
#> 15 -72.28425, 41.00068
#> 16   -72.1862, 41.0344
#> 17 -72.49992, 40.89483
#> 18 -72.44713, 41.01513
#> 19 -72.47195, 40.98980
#> 20 -72.34915, 41.11078
#> 21 -72.37360, 41.07082
#> 22 -72.37558, 41.07012
#> 23 -72.35878, 41.08598
#> 24 -72.37583, 41.09417
#> 25 -72.56870, 40.94198
#> 26 -72.48165, 40.89703
#> 27 -72.53128, 40.97738
#> 28 -72.33427, 41.04942

The beaches can be mapped as follows:

library(mapview)
mapview(beaches)

The pathogen data for these beaches can be imported using the read_pepent() function. This function retrieves data directly from an ArcGIS REST service available at https://gis.suffolkcountyny.gov/hosted/rest/services/Hosted/Beach_Water_Quality_Data/FeatureServer/. The API is queried by beach names in the beaches data object. The queries are done individually for each beach to not exceed the 2000 record limit. A spreadhseet including the same data can also be downloaded from here.

The import function is used as follows:

entdat <- read_pepent()
head(entdat)

#>                    Name FieldNum       Date value status
#> 1 Alberts Landing Beach      EH7 2010-06-29     4      =
#> 2 Alberts Landing Beach      EH7 2010-07-27     4      =
#> 3 Alberts Landing Beach      EH7 2010-08-13    28      =
#> 4 Alberts Landing Beach      EH7 2011-06-22     4      =
#> 5 Alberts Landing Beach      EH7 2011-07-20     4      =
#> 6 Alberts Landing Beach      EH7 2011-08-17     4      =

The data can also be imported from a local file using the path argument.

entdat <- read_pepent(path = '~/Desktop/pathogen_data.xlsx')

The raw data includes concentrations of Enterococcus bacteria as cfu/100 mL for swimming beaches in Suffolk County. The fields include beach name (Name), field number (FieldNum), collection date and time (Date as Eastern Standard Time), bacteria concentration (value), and status showing if the observation was above or below detection (indicated as > or <).

The function anlz_entpep() summarizes the imported data at each beach to quantify instances when bacterial concentrations were at risk of impacting human health. For Suffolk County, all bathing beaches are ranked by relative risk of exposure to harmful bacteria. Factors considered in the ranking include pollution threats (outfalls, discharges, runoff, marinas, etc.), beach location, historical monitoring data, and beach use. Most beaches in the Peconic Estuary are Tier 3 (lowest tier). For the peptools package, the Enterococcus data were used to count the number of instances at each beach when concentrations were above 104 cfu/ml. Although this does not mean a beach was closed, relative exceedances provide a coarse measure of potential risk of exposure to harmful pathogens.

The anlz_entpep() function estimates this exposure risk by counting the number of instances in a year when concentrations at a beach exceeded the threshold for each 24 hour period in the dataset. The results show samples for number of days sampled each year and number of exceedances for the samples. Only the 28 relevant beaches for the Peconic Estuary are returned.

anlz_entpep(entdat)
#> # A tibble: 391 × 4
#>    Name               yr samples exceedances
#>    <chr>           <dbl>   <int>       <int>
#>  1 Alberts Landing  2010       3           0
#>  2 Alberts Landing  2011       3           0
#>  3 Alberts Landing  2012       4           0
#>  4 Alberts Landing  2013       3           0
#>  5 Alberts Landing  2014       4           0
#>  6 Alberts Landing  2015       3           0
#>  7 Alberts Landing  2016       5           0
#>  8 Alberts Landing  2017       3           0
#>  9 Alberts Landing  2018       6           1
#> 10 Alberts Landing  2019       3           0
#> # ℹ 381 more rows

The anlz_entpep() function includes an optional arguments for the threshold (thr). The default values are 104 cfu/100 mL, which can easily be changed. Here we use a threshold of 50 cfu/100 mL.

anlz_entpep(entdat, thr = 50)
#> # A tibble: 391 × 4
#>    Name               yr samples exceedances
#>    <chr>           <dbl>   <int>       <int>
#>  1 Alberts Landing  2010       3           0
#>  2 Alberts Landing  2011       3           0
#>  3 Alberts Landing  2012       4           0
#>  4 Alberts Landing  2013       3           0
#>  5 Alberts Landing  2014       4           0
#>  6 Alberts Landing  2015       3           0
#>  7 Alberts Landing  2016       5           0
#>  8 Alberts Landing  2017       3           0
#>  9 Alberts Landing  2018       6           1
#> 10 Alberts Landing  2019       3           0
#> # ℹ 381 more rows

Plotting results

A summary graphic can be plotted using the show_entmatrix() function. This creates an annual reporting matrix for the relative risk of pathogen exposure at 28 selected beaches in the Peconic Estuary. Tracking the number of exceedances of bacterial concentrations provides a framework for identifying locations that may need management actions to remediate potential public health issues.

show_entmatrix(entdat)

Exceedances of Enterococcus concentrations at Peconic Estuary bathing beaches for the years 2010 through 2023. Values are number of samples exceeding.

The anlz_entpep() function is used internally in show_entmatrix(), such that the optional argument for the threshold (thr) also applies in the plotting function. Appropriate thresholds should be identified. Potential alternatives can be viewed by using a different value for the thr argument.

show_entmatrix(entdat, thr = 35)

Exceedances of Enterococcus concentrations at Peconic Estuary bathing beaches for the years 2010 through 2023. A different option is used for the threshold argument.

The matrix is also a ggplot object and its layout can be changed using ggplot elements. Note the use of txtsz = NULL to remove the text labels.

show_entmatrix(entdat, txtsz = NULL) +
  scale_x_discrete(expand = c(0,0), breaks = c(2000:2023)) + 
  coord_flip() +
  theme(axis.text.x = element_text(angle = 60, hjust = 1, size = 7))