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

Usage

show_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,
  txtsz = 3,
  asreact = FALSE,
  nrows = 10,
  family = NA,
  angle = 90,
  size = 10,
  hjust = 0,
  plotly = FALSE,
  width = NULL,
  height = NULL,
  warn = TRUE
)

Arguments

fibdata: input data frame as returned by read_importfib, read_importentero, or read_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 stas if 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_threshold and temporal_window? Defaults to "all", which will not subset. If "wet" or "dry" is specified, anlz_fibwetdry is 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 object catchprecip has this data from 1995-2023 for select Enterococcus stations. If NULL, defaults to catchprecip.
temporal_window: numeric; required if subset_wetdry is 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_wetdry is not "all". inches accumulated through the defined temporal window, above which a sample should be defined as being from a 'wet' time period
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
angle: numeric for angle of x-axis text labels
size: numeric for size of the x-axis text labels
hjust: numeric for horizontal justification of x-axis 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
warn: logical to print warnings about stations with insufficient data, default 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 410 CFU / 100 mL for E. coli (fresh) or 130 CFU / 100 mL for Enterococcus (marine). Bay segments are used instead of stations if bay_segment is not NULL and the input data are from read_importentero. 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.

See anlz_fibmatrix for additional details on the arguments.

Examples

show_fibmatrix(fibdata)


# show matrix for only dry samples
show_fibmatrix(enterodata, lagyr = 1, subset_wetdry = "dry",
               temporal_window = 2, wet_threshold = 0.5)
#> Warning: Stations with insufficient data for lagyr: 21FLPDEM_WQX-05-06