show_transectavespp: Show annual averages of seagrass frequency occurrence by bay...

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

Show annual averages of seagrass frequency occurrence by bay segments, year, and species

Description

Show annual averages of seagrass frequency occurrence by bay segments, year, and species

Usage

show_transectavespp(
  transectocc,
  bay_segment = c("OTB", "HB", "MTB", "LTB", "BCB"),
  yrrng = c(1998, 2024),
  species = c("Halodule", "Syringodium", "Thalassia", "Halophila", "Ruppia", "Caulerpa",
    "Dapis", "Chaetomorpha"),
  total = TRUE,
  alph = 1,
  family = NA,
  plotly = FALSE,
  asreact = FALSE,
  width = NULL,
  height = NULL,
  sppcol = NULL
)

Arguments

transectocc	data frame returned by anlz_transectocc
bay_segment	chr string for the bay segment, one to many of "OTB", "HB", "MTB", "LTB", "BCB"
yrrng	numeric indicating year ranges to evaluate
species	chr string of species to summarize, one to many of "Halodule", "Syringodium", "Thalassia", "Ruppia", "Halophila", "Caulerpa", "Dapis", "Chaetomorpha"
total	logical indicating if total frequency occurrence for all seagrass species is also returned, only applies if asreact = FALSE
alph	numeric indicating alpha value for score category colors
family	optional chr string indicating font family for text labels
plotly	logical if matrix is created using plotly
asreact	logical if a reactable table is returned instead of a plot
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
sppcol	character vector of alternative colors to use for each species, must have length of six

Details

Results are based on averages across seagrass species (Halodule, Syringodium, Thalassia, Ruppia, Halophila) by date and transect in each bay segment. Drift or attached macroalgae (e.g., Caulerpa, Chaetomorpha) and cyanobacteria (Dapis) estimates may not be accurate prior to 2021. If total = TRUE, a line showing the total frequency occurrence for all seagrass species is also shown (does not include macroalgae or cyanobacteria).

Value

If asreact = F, a ggplot or plotly (if plotly = T) object is returned showing trends over time by species for selected bay segments. If asreact = T, a reactable table showing results by year, segment, and species is returned.

References

The plot is a representation of figure 2 in Johansson, R. (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.

The table is a representation of table 2, p. 163 in Yarbro, L. A., and P. R. Carlson, Jr., eds. 2016. Seagrass Integrated Mapping and Monitoring Program: Mapping and Monitoring Report No. 2. Fish and Wildlife Research Institute Technical Report TR-17 version 2. vi + 281 p.

Examples

## Not run: 
transect <- read_transect()

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

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