threshold_summary: Summary Plots for Threshold Identification

In SWMPrExtension: Functions for Analyzing and Plotting Estuary Monitoring Data

Summary Plots for Threshold Identification

Description

Summary plots for threshold identification analysis

Usage

threshold_summary(swmpr_in, ...)

## S3 method for class 'swmpr'
threshold_summary(
  swmpr_in,
  param = NULL,
  summary_type = c("month", "season", "year"),
  parameter_threshold = NULL,
  threshold_type = NULL,
  time_threshold = NULL,
  converted = FALSE,
  pal = "Set3",
  plot_title = FALSE,
  plot = TRUE,
  label_y_axis = TRUE,
  ...
)

Arguments

swmpr_in	input swmpr object
...	additional arguments passed to other methods. See assign_season for more details.
param	chr string of variable to plot (one only)
summary_type	Choose from month, season, or year aggregation
parameter_threshold	vector of numerical thresholds to evaluate parameters against
threshold_type	vector of logical operators ('<', '>', '<=', '>=', '==', '!=')
time_threshold	The amount of time an event must last to be counted (in hours)
converted	logical, were the units converted from the original units used by CDMO? Defaults to FALSE. See y_labeler for details.
pal	Select a palette for boxplot fill colors. See scale_fill_brewer for more details.
plot_title	logical, should the station name be included as the plot title? Defaults to FALSE
plot	logical, should a plot be returned? Defaults to TRUE
label_y_axis	logical, include label for y-axis?

Details

This function provides a graphical or tabular summary of the results from threshold_identification. The user can summarize results on a monthly, seasonal, or annual basis by specifying summary_type = c('month', 'season', 'year'). If summary_type = 'season', then the user should also define season, season_names, and season_start, as required by |codeassign_season. The user can specify 'month' for nutrient parameters, but this is not recommended and will produce a warning.

Recommended thresholds for chlorophyll-a, dissolved inorganic nitrogen, dissolved inorganic phosphorus, and dissolved oxygen can be found in the National Coastal Condition Assessment 2010 (USEPA 2016)

Value

Returns a ggplot object (if plot = TRUE) or a dataframe (if plot = FALSE)

Author(s)

Julie Padilla

References

United States Environmental Protection Agency (USEPA). 2015. "National Coastal Condition Assessment 2010". EPA 841-R-15-006. https://cfpub.epa.gov/si/si_public_record_Report.cfm?Lab=OWOW&dirEntryId=327030

See Also

assign_season, ggplot, threshold_identification, scale_fill_brewer

Examples

## Water quality examples
data(apacpwq)
dat_wq <- qaqc(apacpwq, qaqc_keep = c(0, 3, 5))
dat_wq <- SWMPr::setstep(dat_wq)

x <-
  threshold_summary(dat_wq, param = 'do_mgl', parameter_threshold = 2
  , threshold_type = '<', time_threshold = 2, summary_type = 'month'
  , plot_title = TRUE)


y <-
  threshold_summary(dat_wq, param = 'do_mgl', parameter_threshold = 2,
  threshold_type = '<', time_threshold = 2, summary_type = 'season',
  season_grps = list(c(1,2,3), c(4,5,6), c(7,8,9), c(10, 11, 12)),
  season_names = c('Winter', 'Spring', 'Summer', 'Fall'),
  season_start = 'Winter',
  plot_title = TRUE)

## Nutrient examples
dat_nut <- qaqc(apacpnut, qaqc_keep = c(0, 3, 5))

x <-
  threshold_summary(dat_nut, param = 'chla_n',
  parameter_threshold = 10,
  threshold_type = '>', summary_type = 'month',
  plot_title = TRUE)

y <-
  threshold_summary(dat_nut, param = 'chla_n', parameter_threshold = 10,
  threshold_type = '>', summary_type = 'season',
  season_grps = list(c(1,2,3), c(4,5,6), c(7,8,9), c(10, 11, 12)),
  season_names = c('Winter', 'Spring', 'Summer', 'Fall'),
  season_start = 'Winter', plot_title = TRUE)

 z <-
   threshold_summary(dat_nut, param = 'chla_n', parameter_threshold = 10,
   threshold_type = '>', summary_type = 'year',
   plot_title = TRUE, plot = TRUE)

SWMPrExtension documentation built on April 21, 2023, 1:14 a.m.