anlz_fibmap: Assign threshold categories to Fecal Indicator Bacteria (FIB)...

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

Assign threshold categories to Fecal Indicator Bacteria (FIB) data

Description

Assign threshold categories to Fecal Indicator Bacteria (FIB) data

Usage

anlz_fibmap(fibdata, yrsel = NULL, mosel = NULL, areasel = NULL, assf = FALSE)

Arguments

fibdata	input FIB data.frame as returned by read_importfib or read_importwqp, see details
yrsel	optional numeric value to filter output by years in fibdata
mosel	optional numeric value to filter output by month in fibdata
areasel	optional character string to filter output by stations in the area column of fibdata, see details
assf	logical indicating if the data are further processed as a simple features object with additional columns for show_fibmap

Details

This function is used to create FIB categories for mapping using show_fibmap. Categories based on relevant thresholds are assigned to each observation. The categories are specific to E. coli or Enterococcus and are assigned based on the station class as freshwater (class as 1 or 3F) or marine (class as 2 or 3M), respectively. 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 input fibdata object can be one returned by either read_importfib or read_importwqp.

The areasel argument can indicate valid entries in the area column of fibdata from read_importfib or mancofibdata, pascofibdata, polcofibdata, or hcesdfibdata from read_importwqp. For example, use either "Alafia River" or "Hillsborough River" to show stations for the corresponding river basins, where rows in fibdata are filtered based on the the selection. All valid options for areasel for fibdata include "Alafia River", "Hillsborough River", "Cockroach Bay", "East Lake Outfall", "Hillsborough Bay", "Little Manatee", "Lower Tampa Bay", "McKay Bay", "Middle Tampa Bay", "Old Tampa Bay", "Palm River", "Tampa Bypass Canal", or "Valrico Lake". Valid options for areasel if the input data are from read_importwqp are any that are present in the area column for the respective input datasets (mancofibdata, pascofibdata, polcofibdata, or polcofibdata). One to any of the options can be used.All stations are returned if this argument is set as NULL (default). Not all areas may be present based on the year/month selection.

Value

A data.frame similar to the input 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_fibmap.

Examples

# assign categories to all
anlz_fibmap(fibdata)

# filter by year, month, and area
anlz_fibmap(fibdata, yrsel = 2020, mosel = 7, areasel = 'Alafia River')

# as sf object
anlz_fibmap(fibdata, assf = TRUE)

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