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, 2024),
  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) { # \dontrun{
transect <- read_transect()
} # }
transectocc <- anlz_transectocc(transect)
show_transectmatrix(transectocc)