Analyze Fecal Indicator Bacteria categories over time by station
Source:R/anlz_fibmatrix.R
anlz_fibmatrix.RdAnalyze Fecal Indicator Bacteria categories over time by station
Arguments
- fibdata
input data frame as returned by
read_importfib- yrrng
numeric vector indicating min, max years to include, defaults to range of years in
epcdata- stas
optional numeric vector of stations to include, see details
- lagyr
numeric for year lag to calculate categories, see details
Value
A tibble object with FIB summaries by year and station, including columns for the estimated geometric mean of fecal coliform concentrations (gmean), the proportions of samples exceeding 400 CFU / 100 mL (exced), the count of samples (cnt), and a category indicating a letter outcome based on the proportion of exceedences (cat).
Details
This function is used to create output for plotting a matrix stoplight graphic for FIB categories by station and year. Each station and year combination is categorized based on the likelihood of fecal indicator bacteria concentrations exceeding 400 CFU / 100 mL in a given year (using Fecal Coliform, fcolif in fibdata). 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.
Examples
anlz_fibmatrix(fibdata)
#> # A tibble: 8,800 × 4
#> yr epchc_station gmean cat
#> <dbl> <fct> <dbl> <chr>
#> 1 1985 2 52.4 B
#> 2 1985 6 7.21 A
#> 3 1985 7 4.64 A
#> 4 1985 8 9.49 A
#> 5 1985 9 6.32 A
#> 6 1985 11 5.18 A
#> 7 1985 13 4 A
#> 8 1985 14 6.35 A
#> 9 1985 16 4 A
#> 10 1985 19 4 A
#> # ℹ 8,790 more rows