show_fibmatrix: Plot a matrix of Fecal Indicator Bacteria categories over...
In tbep-tech/tbeptools: Data and Indicators for the Tampa Bay Estuary Program

show_fibmatrix

R Documentation

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

Description

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`

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.

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.

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)

tbep-tech/tbeptools documentation built on April 13, 2025, 4:50 p.m.