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Show matrix of seagrass frequency occurrence by bay segments and year

Usage

show_transectmatrix(
  transectocc,
  bay_segment = c("OTB", "HB", "MTB", "LTB", "BCB"),
  total = TRUE,
  neutral = FALSE,
  yrrng = c(1998, 2021),
  alph = 1,
  txtsz = 3,
  family = NA,
  rev = FALSE,
  position = "top",
  plotly = FALSE,
  width = NULL,
  height = NULL
)

Arguments

transectocc

data frame returned by anlz_transectocc

bay_segment

chr string for the bay segment, one to many of "HB", "OTB", "MTB", "LTB", "TCB", "MR", "BCB"

total

logical indicating if average frequency occurrence is calculated for the entire bay across segments

neutral

logical indicating if a neutral and continuous color scheme is used

yrrng

numeric indicating year ranges to evaluate

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 of plotly = TRUE

height

numeric for height of the plot in pixels, only applies of plotly = TRUE

Value

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

Details

Results are based on averages across species by date and transect in each bay segment

The color scheme is based on arbitrary breaks at 25, 50, and 75 percent frequency occurrence. These don't necessarily translate to any ecological breakpoints. Use neutral = TRUE to use a neutral and continuous color palette.

References

This plot is a representation of Table 1 in R. Johansson (2016) Seagrass Transect Monitoring in Tampa Bay: A Summary of Findings from 1997 through 2015, Technical report #08-16, Tampa Bay Estuary Program, St. Petersburg, Florida.

Examples

if (FALSE) {
transect <- read_transect()
}
transectocc <- anlz_transectocc(transect)
show_transectmatrix(transectocc)