Analyze Fecal Indicator Bacteria categories over time by station or bay segment
Source:R/anlz_fibmatrix.R
anlz_fibmatrix.RdAnalyze Fecal Indicator Bacteria categories over time by station or bay segment
Usage
anlz_fibmatrix(
fibdata,
yrrng = NULL,
stas = NULL,
bay_segment = NULL,
lagyr = 3,
subset_wetdry = c("all", "wet", "dry"),
precipdata = NULL,
temporal_window = NULL,
wet_threshold = NULL,
warn = TRUE
)Arguments
- fibdata
input data frame as returned by
read_importfib,read_importentero, orread_importwqp, see details- yrrng
numeric vector indicating min, max years to include, defaults to range of years in data, see details
- stas
optional vector of stations to include, see details
- bay_segment
optional vector of bay segment names to include, supercedes
stasif provided, see details- lagyr
numeric for year lag to calculate categories, see details
- subset_wetdry
character, subset data frame to only wet or dry samples as defined by
wet_thresholdandtemporal_window? Defaults to"all", which will not subset. If"wet"or"dry"is specified,anlz_fibwetdryis called using the further specified parameters, and the data frame is subsetted accordingly.- precipdata
input data frame as returned by
read_importrain. columns should be: station, date (yyyy-mm-dd), rain (in inches). The objectcatchpreciphas this data from 1995-2023 for select Enterococcus stations. IfNULL, defaults tocatchprecip.- temporal_window
numeric; required if
subset_wetdryis not"all". number of days precipitation should be summed over (1 = day of sample only; 2 = day of sample + day before; etc.)- wet_threshold
numeric; required if
subset_wetdryis not"all". inches accumulated through the defined temporal window, above which a sample should be defined as being from a 'wet' time period- warn
logical to print warnings about stations with insufficient data, default
TRUE
Value
A tibble object with FIB summaries by year and station including columns for the estimated geometric mean of Enterococcus (marine) or E. coli (fresh) concentrations (gmean), the proportion of samples exceeding 130 CFU / 100 mL (Enterococcus) or 410 CFU / 100 mL (exced), the count of samples (cnt), and a category indicating a letter outcome based on the proportion of exceedences (cat). Results can be summarized by bay segment if bay_segment is not NULL and the input data is from read_importentero.
Details
This function is used to create output for plotting a matrix stoplight graphic for FIB categories by station. The output can also be summarized by bay segment if bay_segment is not NULL and the input data is from read_importentero. In the latter case, the stas argument is ignored and all stations within each subsegment watershed are used to evaluate the FIB categories. Each station (or bay segment) and year combination is categorized based on the likelihood of fecal indicator bacteria concentrations exceeding some threshold in a given year. For Enterococcus (marine), the default threshold is 130 CFU / 100 mL in a given year. For E. coli (fresh), the default threshold is 410 CFU / 100 mL. The proportions 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). 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 using the monthly samples (lagyr = 3). See show_fibmatrix for additional details.
yrrng can be specified several ways. If yrrng = NULL, the year range of the data for the selected changes is chosen. User-defined values for the minimum and maximum years can also be used, or only a minimum or maximum can be specified, e.g., yrrng = c(2000, 2010) or yrrng = c(2000, NA). In the latter case, the maximum year will be defined by the data.
The default stations if the input is fibdata are those used in TBEP report #05-13 (https://drive.google.com/file/d/1MZnK3cMzV7LRg6dTbCKX8AOZU0GNurJJ/view) for the Hillsborough River Basin Management Action Plan (BMAP) subbasins if bay_segment is NULL and the input data are from read_importfib. 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 can be plotted using the stas argument.
Input from read_importwqp for Manatee County (21FLMANA_WQX) FIB data can also be used. The function has not been tested for other organizations.
Examples
anlz_fibmatrix(fibdata)
#> # A tibble: 102 × 7
#> yr grp class gmean Latitude Longitude cat
#> <dbl> <fct> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 2003 105 Marine 97.1 28.0 -82.4 C
#> 2 2003 152 Marine 266. 28.0 -82.5 D
#> 3 2003 137 Marine 342. 28.0 -82.5 D
#> 4 2004 105 Marine 216. 28.0 -82.4 C
#> 5 2004 152 Marine 246. 28.0 -82.5 C
#> 6 2004 137 Marine 302. 28.0 -82.5 D
#> 7 2005 105 Marine 117. 28.0 -82.4 C
#> 8 2005 152 Marine 91.7 28.0 -82.5 C
#> 9 2005 137 Marine 66.6 28.0 -82.5 C
#> 10 2006 105 Marine 90.7 28.0 -82.4 C
#> # ℹ 92 more rows
# use different dataset
anlz_fibmatrix(enterodata, lagyr = 1)
#> Warning: Stations with insufficient data for lagyr: 21FLPDEM_WQX-05-06
#> # A tibble: 643 × 7
#> yr grp class gmean Latitude Longitude cat
#> <dbl> <fct> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 2000 21FLDOH_WQX-MANATEE152 Marine 10.7 27.5 -82.7 A
#> 2 2001 21FLDOH_WQX-MANATEE152 Marine 16.0 27.5 -82.7 A
#> 3 2001 21FLHILL_WQX-101 Marine 284. 28.0 -82.6 C
#> 4 2001 21FLHILL_WQX-102 Marine 55.7 28.0 -82.6 A
#> 5 2001 21FLHILL_WQX-103 Marine 214. 28.0 -82.6 B
#> 6 2001 21FLHILL_WQX-104 Marine 408. 28.0 -82.6 D
#> 7 2001 21FLHILL_WQX-109 Marine 97.8 27.9 -82.4 B
#> 8 2001 21FLHILL_WQX-112 Marine 48.3 27.7 -82.4 A
#> 9 2001 21FLHILL_WQX-133 Marine 747. 27.9 -82.4 D
#> 10 2001 21FLHILL_WQX-136 Marine 26.1 27.7 -82.5 A
#> # ℹ 633 more rows
# subset to only wet samples
anlz_fibmatrix(enterodata, lagyr = 1, subset_wetdry = "wet",
temporal_window = 2, wet_threshold = 0.5)
#> # A tibble: 466 × 7
#> yr grp class gmean Latitude Longitude cat
#> <dbl> <fct> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 2001 21FLDOH_WQX-MANATEE152 Marine 31.6 27.5 -82.7 A
#> 2 2001 21FLHILL_WQX-101 Marine 2252. 28.0 -82.6 C
#> 3 2001 21FLHILL_WQX-102 Marine 66.0 28.0 -82.6 A
#> 4 2001 21FLHILL_WQX-103 Marine 472. 28.0 -82.6 B
#> 5 2001 21FLHILL_WQX-104 Marine 3284. 28.0 -82.6 C
#> 6 2001 21FLHILL_WQX-109 Marine 133. 27.9 -82.4 A
#> 7 2001 21FLHILL_WQX-112 Marine 40 27.7 -82.4 A
#> 8 2001 21FLHILL_WQX-133 Marine 3286. 27.9 -82.4 C
#> 9 2002 21FLDOH_WQX-MANATEE152 Marine 13.7 27.5 -82.7 A
#> 10 2002 21FLHILL_WQX-101 Marine 531. 28.0 -82.6 C
#> # ℹ 456 more rows
# Manatee County data
anlz_fibmatrix(mancofibdata, lagyr = 1)
#> # A tibble: 200 × 7
#> yr grp class gmean Latitude Longitude cat
#> <dbl> <fct> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 2013 LM4 Marine 771. 27.5 -82.5 C
#> 2 2014 LM3 Marine 161 27.5 -82.5 A
#> 3 2014 LM4 Marine 387 27.5 -82.5 A
#> 4 2015 LM3 Marine 259. 27.5 -82.5 C
#> 5 2015 LM4 Marine 222. 27.5 -82.5 C
#> 6 2016 LM4 Marine 2419 27.5 -82.5 A
#> 7 2017 LM3 Marine 1553 27.5 -82.5 A
#> 8 2018 BC1 Fresh 1591. 27.4 -82.6 C
#> 9 2018 BC2 Fresh 674. 27.4 -82.6 C
#> 10 2018 BR1 Fresh 16.6 27.4 -82.5 A
#> # ℹ 190 more rows