# Threshold Percentile Plot Observed data compared against user-defined percentiles ```r 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` ## Returns Returns a `ggplot` object ## 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) ## Examples ```r 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) ``` ## 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` ## Author(s) Julie Padilla

threshold_percentile_plot function