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 similar to the input 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.
The input fibdata object can be one returned by either read_importfib or read_importwqp.
The areasel argument can indicate valid entries in the area column of fibdata from read_importfib or mancofibdata, pascofibdata, polcofibdata, or hcesdfibdata from read_importwqp. For example, use either "Alafia River" or "Hillsborough River" to show stations for the corresponding river basins, where rows in fibdata are filtered based on the the selection. All valid options for areasel for fibdata include "Alafia River", "Hillsborough River", "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". Valid options for areasel if the input data are from read_importwqp are any that are present in the area column for the respective input datasets (mancofibdata, pascofibdata, polcofibdata, or polcofibdata). One to any of the options can be used.All stations are returned if this argument is set as NULL (default). Not all areas may be present based on the year/month selection.
Examples
# assign categories to all
anlz_fibmap(fibdata)
#> # A tibble: 29,175 × 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 12 27.9 -82.5 NA 28 Ente… < 35
#> 2 Hillsb… 6 3M 2024 12 27.9 -82.5 NA 2 Ente… < 35
#> 3 Hillsb… 7 3M 2024 12 27.9 -82.5 NA 2 Ente… < 35
#> 4 Hillsb… 8 3M 2024 12 27.9 -82.4 NA 2 Ente… < 35
#> 5 Middle… 9 2 2024 12 27.8 -82.4 NA 4 Ente… < 35
#> 6 Middle… 11 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 7 Middle… 13 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 8 Middle… 14 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 9 Middle… 16 2 2024 12 27.7 -82.5 NA 2 Ente… < 35
#> 10 Middle… 19 2 2024 12 27.7 -82.6 NA 2 Ente… < 35
#> # ℹ 29,165 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: 13 × 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 …
#> 11 Alafia… 166 3F 2020 7 27.9 -82.2 310 480 E. c… 126 …
#> 12 Alafia… 178 3M 2020 7 27.9 -82.4 NA 650 Ente… 130 …
#> 13 Alafia… 179 3M 2020 7 27.9 -82.3 NA 1010 Ente… > 999
#> # ℹ 1 more variable: col <chr>
# as sf object
anlz_fibmap(fibdata, assf = TRUE)
#> Simple feature collection with 29175 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: 29,175 × 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 12 27.9 -82.5 NA 28 Ente… < 35
#> 2 Hillsb… 6 3M 2024 12 27.9 -82.5 NA 2 Ente… < 35
#> 3 Hillsb… 7 3M 2024 12 27.9 -82.5 NA 2 Ente… < 35
#> 4 Hillsb… 8 3M 2024 12 27.9 -82.4 NA 2 Ente… < 35
#> 5 Middle… 9 2 2024 12 27.8 -82.4 NA 4 Ente… < 35
#> 6 Middle… 11 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 7 Middle… 13 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 8 Middle… 14 2 2024 12 27.8 -82.5 NA 2 Ente… < 35
#> 9 Middle… 16 2 2024 12 27.7 -82.5 NA 2 Ente… < 35
#> 10 Middle… 19 2 2024 12 27.7 -82.6 NA 2 Ente… < 35
#> # ℹ 29,165 more rows
#> # ℹ 6 more variables: col <chr>, geometry <POINT [°]>, grp <fct>, conc <dbl>,
#> # cls <chr>, lab <chr>