anlz_enteromap: Assign threshold categories to Enterococcus data

In tbep-tech/tbeptools: Data and Indicators for the Tampa Bay Estuary Program

Assign threshold categories to Enterococcus data

Description

Assign threshold categories to Enterococcus data

Usage

anlz_enteromap(
  fibdata,
  yrsel = NULL,
  mosel = NULL,
  areasel = NULL,
  wetdry = FALSE,
  precipdata = NULL,
  temporal_window = NULL,
  wet_threshold = NULL,
  assf = FALSE
)

Arguments

fibdata	data frame of Enterococcus sample data as returned by enterodata or anlz_fibwetdry
yrsel	optional numeric to filter data by year
mosel	optional numeric to filter data by month
areasel	optional character string to filter output by stations in the long_name column of enterodata, see details
wetdry	logical; if TRUE, incorporate wet/dry differences (this will result in a call to anlz_fibwetdry, in which case temporal_window and wet_threshold are required). If FALSE (default), do not differentiate between wet and dry samples.
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 wetdry is TRUE. 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 wetdry is TRUE. inches accumulated through the defined temporal window, above which a sample should be defined as being from a 'wet' time period
assf	logical indicating if the data are further processed as a simple features object with additional columns for show_enteromap

Details

This function is based on anlz_fibmap, but is specific to Enterococcus data downloaded via read_importentero. It creates categories for mapping using show_enteromap. Optionally, if samples have been defined as 'wet' or not via anlz_fibwetdry, this can be represented via symbols on the map. Categories based on relevant thresholds are assigned to each observation. The categories are specific to Enterococcus in marine waters (class of 2 or 3M). A station is categorized into one of four ranges defined by the thresholds as noted in the cat column of the output, with corresponding colors appropriate for each range as noted in the col column of the output.

The areasel argument can indicate valid entries in the long_name column of enterodata. For example, use "Old Tampa Bay" for stations in the subwatershed of Old Tampa Bay, where rows in enterodata are filtered based on the the selection. All stations are returned if this argument is set as NULL (default). All valid options for areasel include "Old Tampa Bay", "Hillsborough Bay", "Middle Tampa Bay", "Lower Tampa Bay", "Boca Ciega Bay", or "Manatee River". One to any of the options can be used.

Value

A data.frame similar to fibdata if assf = FALSE with additional columns describing station categories and optionally filtered by arguments passed to the function. A sf object if assf = TRUE with additional columns for show_enteromap.

Examples

anlz_enteromap(enterodata, yrsel = 2020, mosel = 9)

# differentiate wet/dry samples in that time frame
anlz_enteromap(enterodata, yrsel = 2020, mosel = 9, wetdry = TRUE,
               temporal_window = 2, wet_threshold = 0.5)

# as sf object
anlz_enteromap(enterodata, assf = TRUE)

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