Overview
rsimplotviz() creates an interactive plotly time series from an
Rsim output object. You can plot all species at once or
focus on individual groups, and toggle between absolute and relative
biomass.
Setting up an Rsim scenario
We use the fictional R Ecosystem (REco.params) bundled
with Rpath.
# Build the balanced Rpath model
REco <- rpath(REco.params, eco.name = "R Ecosystem")
# Create an Rsim scenario and run it for 50 years
scene <- rsim.scenario(REco, REco.params, years = 1:50)
Rsim.output <- rsim.run.patched(scene, years = 1:50)Plot all species — relative biomass
When spname = "all" (the default), all species are
plotted as relative biomass (biomass relative to the starting value).
Use the legend to toggle individual species on and off.
rsimplotviz(Rsim.output, eco.name = "R Ecosystem", spname = "all",
palette = "rsim_pal_dark")Light color palette
Switch to "rsim_pal_light" for a softer, pastel
look.
rsimplotviz(Rsim.output, eco.name = "R Ecosystem", spname = "all",
palette = "rsim_pal_light")Single species — absolute biomass
To examine one species in its original biomass units, pass its name
to spname and set rel_bio = FALSE.
rsimplotviz(Rsim.output, eco.name = "R Ecosystem",
spname = "Foragefish2",
rel_bio = FALSE)Single species — relative biomass
Setting rel_bio = TRUE rescales the single species to
its starting biomass, making it easy to compare trends across species or
scenarios.
rsimplotviz(Rsim.output, eco.name = "R Ecosystem",
spname = "Foragefish2",
rel_bio = TRUE)Custom color palette
Supply any vector of hex colors. rsimplotviz() will
interpolate if you provide fewer colors than there are species.
my_pal <- c("#264653", "#2a9d8f", "#e9c46a", "#f4a261", "#e76f51",
"#023e8a", "#8ecae6", "#219ebc", "#023047", "#ffb703")
rsimplotviz(Rsim.output, eco.name = "R Ecosystem", palette = my_pal)