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 = "sans",
  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). 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.

Bay segments scores are used instead of stations if bay_segment is not NULL and the input data are from read_importentero. Care should be taken when communicating results at the bay segment scale to ensure appropriate messaging. Baywide scores could be misleading by using a handful of stations to communicate results at the bay segment scale. Reporting at this scale is meant to support assessments that are comparable to other similar indicators used by TBEP. A low grade for a bay segment does not imply hazardous conditions, rather the score reflects the aggregate likelihood for all stations selected for that bay segment. Remediation of conditions that contribute to fecal contamination is best handled at the site scale.

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