Assign threshold categories to Fecal Indicator Bacteria (FIB) data
Source:R/anlz_fibmap.R
anlz_fibmap.RdAssign threshold categories to Fecal Indicator Bacteria (FIB) data
Arguments
- fibdata
input FIB
data.frameas returned byread_importfiborread_importwqp, see details- yrsel
optional numeric value to filter output by years in
fibdata- mosel
optional numeric value to filter output by month in
fibdata- areasel
optional character string to filter output by stations in the
areacolumn offibdata, see details- assf
logical indicating if the data are further processed as a simple features object with additional columns for
show_fibmap
Value
A data.frame if similar to fibdata or mancofibdata if assf = FALSE with additional columns describing station categories and optionally filtered by arguments passed to the function. A sf object if assf = TRUE with additional columns for show_fibmap.
Details
This function is used to create FIB categories for mapping using show_fibmap. Categories based on relevant thresholds are assigned to each observation. 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.
Data from Manatee County (21FLMANA_WQX) returned by read_importwqp can be used with this function. Data from other organizations returned by this function have not been tested.
The areasel argument can indicate valid entries in the area column of fibdata (from read_importfib) or mancofibdata (from read_importwqp). For example, use either "Alafia River" or "Hillsborough River" for the corresponding river basins, where rows in fibdata are filtered based on the the selection. All stations are returned if this argument is set as 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.
All valid options for areasel for fibdata 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". One to any of the options can be used.
Valid entries for areasel for mancofibdata include "Big Slough", "Bowlees Creek", "Braden River", "Bud Slough", "Clay Gully", "Frog Creek", "Gap Creek", "Little Manatee River", "Lower Tampa Bay", "Manatee River", "Mcmullen Creek", "Mud Lake Slough", "Myakka River", "Palma Sola Bay", or "Piney Point Creek". One to any of the options can be used.
Examples
# assign categories to all
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>
# filter by year, month, and area
anlz_fibmap(fibdata, yrsel = 2020, mosel = 7, areasel = 'Alafia River')
#> # A tibble: 24 × 12
#> area station class yr mo Latitude Longitude ecoli entero ind cat
#> <chr> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <fct>
#> 1 Alafia… 74 3M 2020 7 27.9 -82.4 NA 168 Ente… 130 …
#> 2 Alafia… 111 3F 2020 7 27.9 -82.2 50 7000 E. c… < 126
#> 3 Alafia… 114 3F 2020 7 27.9 -82.3 447 1560 E. c… 410 …
#> 4 Alafia… 115 3F 2020 7 27.9 -82.1 80 260 E. c… < 126
#> 5 Alafia… 116 3F 2020 7 27.9 -82.1 30 367 E. c… < 126
#> 6 Alafia… 139 3F 2020 7 27.7 -82.1 47 100 E. c… < 126
#> 7 Alafia… 151 3F 2020 7 27.9 -82.2 90 25 E. c… < 126
#> 8 Alafia… 153 3M 2020 7 27.9 -82.3 NA 4000 Ente… > 999
#> 9 Alafia… 154 3F 2020 7 27.9 -82.1 433 1367 E. c… 410 …
#> 10 Alafia… 155 3F 2020 7 27.9 -82.2 170 233 E. c… 126 …
#> # ℹ 14 more rows
#> # ℹ 1 more variable: col <chr>
# as sf object
anlz_fibmap(fibdata, assf = TRUE)
#> Simple feature collection with 28287 features and 16 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: -82.7832 ymin: 27.53248 xmax: -82.05604 ymax: 28.16544
#> Geodetic CRS: WGS 84
#> # A tibble: 28,287 × 17
#> 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 28,277 more rows
#> # ℹ 6 more variables: col <chr>, geometry <POINT [°]>, grp <fct>, conc <dbl>,
#> # cls <chr>, lab <chr>