Plot a matrix of AMBI scores over time by bay segment

Usage

show_ambimatrix(
  ambiscr,
  bay_segment = c("HB", "OTB", "MTB", "LTB", "TCB", "MR", "BCB", "All"),
  yrrng = c(1993, 2024),
  window = TRUE,
  alph = 1,
  txtsz = 2.5,
  family = "sans",
  rev = FALSE,
  position = "top",
  plotly = FALSE,
  width = NULL,
  height = NULL
)

Arguments

ambiscr: input data frame as returned by anlz_ambiscr; the AMBI variant is detected automatically from the column names
bay_segment: chr string for the bay segment, one to many of "HB", "OTB", "MTB", "LTB", "TCB", "MR", "BCB", "All"
yrrng: numeric indicating year ranges to evaluate
window: logical indicating whether to use a rolling 5-year window (default TRUE) or single year values (FALSE) for the bay segment categories, see details
alph: numeric indicating alpha value for score category colors
txtsz: numeric for size of text in the plot
family: optional chr string indicating font family for text labels
rev: logical if factor levels for bay segments are reversed
position: chr string of location for bay segment labels, default on top, passed to scale_x_discrete
plotly: logical if matrix is created using plotly
width: numeric for width of the plot in pixels, only applies if plotly = TRUE
height: numeric for height of the plot in pixels, only applies if plotly = TRUE

Value

A ggplot object showing trends over time in AMBI scores for each bay segment if plotly = FALSE, otherwise a plotly object

Details

An additional summary is provided for the entire bay as an unweighted summary across categories ("All").

The default behavior is to use a rolling five-year window to calculate the percent of sites in each AMBI category by bay segment. This applies only to years 2005 and later, where the counts from the current year and the prior four years are summed to calculate the percentages. This is intended to help smooth out inter-annual variability due to reduced sampling effort from 2005 to present. If window = FALSE, then only single year values are used.

The color scale reflects the adjusted AMBI classification (0-10 scale): Unpolluted (dark green), Slightly Polluted (light green), Meanly Polluted (yellow), Heavily Polluted (orange), and Extremely Polluted (red).

The matrix tile for each bay segment and year shows the dominant AMBI category based on the plurality of sites. The dominant category is the one with the highest proportion of sites in that year and bay segment.

Examples

ambiscr <- anlz_ambiscr(benthicdata)
show_ambimatrix(ambiscr)