Plot a matrix of Fecal Indicator Bacteria categories over time by station

Usage

show_fibmatrix(
  fibdata,
  yrrng = NULL,
  stas = c(143, 108, 107, 135, 118, 148, 105, 152, 137),
  lagyr = 3,
  txtsz = 3,
  asreact = FALSE,
  nrows = 10,
  family = NA,
  plotly = FALSE,
  width = NULL,
  height = NULL
)

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
txtsz: numeric for size of text in the plot, applies only if tab = FALSE. Use txtsz = NULL to suppress.
asreact: logical indicating if a reactable object is returned
nrows: if asreact = TRUE, a numeric specifying number of rows in the table
family: optional chr string indicating font family for text labels
plotly: logical if matrix is created using plotly
width: numeric for width of the plot in pixels, only applies of plotly = TRUE
height: numeric for height of the plot in pixels, only applies of plotly = TRUE

Value

A static ggplot object is returned by default. A reactable table is returned if asreact = TRUE. An interactive plotly object is returned if plotly = TRUE.

Details

The matrix color codes years and stations based on the likelihood of fecal indicator bacteria concentrations exceeding 400 CFU / 100 mL (using Fecal Coliform, fcolif in fibdata). The likelihoods 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 from the monthly samples (lagyr = 3). Methods and rationale for this categorization scheme are provided by the Florida Department of Environmental Protection, Figure 8 in the document at http://publicfiles.dep.state.fl.us/DEAR/BMAP/Tampa/MST%20Report/Fecal%20BMAP%20DST%20Final%20Report%20--%20June%202008.pdf and Morrison et al. 2009 in the BASIS 5 proceedings.

The default stations 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. 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 in fibdata can be plotted using the stas argument.

Examples

show_fibmatrix(fibdata)