
Show annual averages of seagrass frequency occurrence by bay segments, year, and species
Source:R/show_transectavespp.R
show_transectavespp.Rd
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.
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)