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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, 2022),
  species = c("Halodule", "Syringodium", "Thalassia", "Halophila", "Ruppia",
    "Caulerpa"),
  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"

total

logical indicating if total frequency occurrence for all 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 species by date and transect in each bay segment

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) {
transect <- read_transect()
}
transectocc <- anlz_transectocc(transect)
show_transectavespp(transectocc)