threshold_percentile_plot: Threshold Percentile Plot

In SWMPrExtension: Functions for Analyzing and Plotting Estuary Monitoring Data

Threshold Percentile Plot

Description

Observed data compared against user-defined percentiles

Usage

threshold_percentile_plot(swmpr_in, ...)

## S3 method for class 'swmpr'
threshold_percentile_plot(
  swmpr_in,
  param = NULL,
  hist_rng = NULL,
  target_yr = NULL,
  percentiles = c(0.05, 0.95),
  free_y = FALSE,
  by_month = FALSE,
  log_trans = FALSE,
  converted = FALSE,
  plot_title = FALSE,
  ...
)

Arguments

swmpr_in	input swmpr object
...	additional arguments passed to other methods (not used for this function).
param	chr, variable to plot
hist_rng	num, years to include in the plot. This variable can either be one year (e.g., hist_rng = 2012), or two years (e.g. hist_rng = c(2012, 2016)) , If range is not specified then the entire data set will be used.
target_yr	num, year of interest for plotting. If not specified, the entire data set will be plotted.
percentiles	num, percentiles to calculate (maximum: 2). Defaults to 5th and 95th percentiles.
free_y	logical, should the y-axis be free? Defaults to FALSE. If FALSE, defaults to zero, unless negative values are present. If TRUE, y-axis limits are selected by ggplot
by_month	logical. should percentiles be calculated on a monthly basis? Defaults to FALSE
log_trans	logical, should y-axis be log? Defaults to FALSE
converted	logical, were the units converted from the original units used by CDMO? Defaults to FALSE. See y_labeler for details.
plot_title	logical, should the station name be included as the plot title? Defaults to FALSE

Details

This function provides an alternative to threshold_criteria_plot. For parameters that may not have numeric threshold criteria, a percentile threshold can be used instead. For a one-tailed analysis, the 90-th percentile is recommended. For a two-tailed analysis, the 5-th and 95-th percentiles are recommended.

Using by_month, the user can specify whether the percentiles should be calculated on a monthly basis or by using the entire data set.

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

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

ggplot

Examples

dat_wq <- qaqc(elksmwq, qaqc_keep = c(0, 3, 5))
dat_wq <- subset(dat_wq, subset = '2007-01-01 0:00', operator = '>=')

x <-
  threshold_percentile_plot(dat_wq, param = 'do_mgl'
                           , hist_rng = c(2013, 2014), by_month = FALSE)


y <-
  threshold_percentile_plot(dat_wq, param = 'do_mgl', percentiles = c(0.95)
                           , hist_rng = c(2013, 2014), target_yr = 2014
                           , by_month = FALSE)

x2 <-
  threshold_percentile_plot(dat_wq, param = 'do_mgl'
                           , hist_rng = c(2013, 2014), by_month = TRUE)

y2 <-
  threshold_percentile_plot(dat_wq, param = 'do_mgl'
                           , hist_rng = c(2013, 2014), by_month = TRUE
                           , target_yr = 2014)


dat_nut <- qaqc(elknmnut, qaqc_keep = c(0, 3, 5))
dat_nut <- subset(dat_nut, subset = '2007-01-01 0:00', operator = '>=')
dat_nut <- rem_reps(dat_nut)

x3 <-
  threshold_percentile_plot(dat_nut, param = 'chla_n'
                           , hist_rng = c(2007, 2014), by_month = FALSE)

y3 <-
  threshold_percentile_plot(dat_nut, param = 'chla_n'
                           , hist_rng = c(2007, 2014), by_month = FALSE
                           , target_yr = 2016)

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