show_transectmatrix: Show matrix of seagrass frequency occurrence by bay segments...

In tbep-tech/tbeptools: Data and Indicators for the Tampa Bay Estuary Program

Show matrix of seagrass frequency occurrence by bay segments and year

Description

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

Details

Results are based on averages across seagrass species (Halodule, Syringodium, Thalassia, Ruppia, Halophila) 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.

Value

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

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

## Not run: 
transect <- read_transect()

## End(Not run)
transectocc <- anlz_transectocc(transect)
show_transectmatrix(transectocc)

tbep-tech/tbeptools documentation built on April 13, 2025, 4:50 p.m.