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

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.

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).

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

if (FALSE) { # \dontrun{
transect <- read_transect()
} # }
transectocc <- anlz_transectocc(transect)
show_transectavespp(transectocc)