Visualising coralseed outputs • coralseed

Overview

This tutorial collects visualisation patterns for coralseed outputs: static ggplot2 maps, package plotting functions, map_coralseed() widgets, flowcharts, and animations.

library(coralseed)
library(tidyverse)
library(sf)
library(ggplot2)
library(tmap)

sf::sf_use_s2(FALSE)

Build a small example simulation

benthic_map <- system.file("extdata", "Lizard_Benthic.geojson", package = "coralseed") |>
  st_read(quiet = TRUE)

reef_map <- system.file("extdata", "Lizard_Geomorphic.geojson", package = "coralseed") |>
  st_read(quiet = TRUE)

seascape <- seascape_probability(reefoutline = reef_map, habitat = benthic_map)

particles_sf <- system.file("extdata", "lizard_del_14_1512_sim1_10.json", package = "coralseed") |>
  st_read(quiet = TRUE)

seeded <- seed_particles(
  input = particles_sf,
  zarr = FALSE,
  set.centre = TRUE,
  seascape = seascape,
  probability = "additive",
  limit.time = 12,
  competency.function = "exponential",
  crs = 20353,
  simulate.mortality = "typeIII",
  simulate.mortality.n = 0.1,
  return.plot = FALSE,
  return.summary = TRUE,
  silent = TRUE
)

settled <- settle_particles(seeded, probability = "additive", return.plot = FALSE, silent = TRUE)
settlement_dens <- settlement_density(settled$points)

Static settlement map

ggplot() +
  geom_sf(data = seascape, aes(fill = settlement_probability), colour = NA, alpha = 0.55) +
  geom_sf(data = settled$points, size = 0.2, alpha = 0.35) +
  scale_fill_viridis_c(na.value = "grey90") +
  labs(
    title = "Settled particles over habitat probability surface",
    fill = "Settlement\nprobability"
  ) +
  theme_bw()

Density map

ggplot() +
  geom_sf(data = seascape, fill = "grey92", colour = NA) +
  geom_sf(data = settlement_dens, aes(colour = n), size = 1.5) +
  scale_colour_viridis_c() +
  labs(
    title = "Settlement density",
    colour = "Settlers"
  ) +
  theme_bw()

Package plot helper

plot_particles(settled$points, seascape)

Interactive map

map_coralseed() creates an interactive output. Keep it eval: false in pkgdown if the widget is slow or unstable during rendering.

map_coralseed(
  seed_particles_input = seeded,
  settle_particles_input = settled,
  settlement_density_input = settlement_dens,
  seascape_probability = seascape,
  restoration.plot = c(100, 100),
  show.footprint = TRUE,
  show.tracks = TRUE,
  subsample = 1000,
  webGL = TRUE
)

Flowchart

flowchart_coralseed(
  seeded,
  settled,
  multiplier = 1000,
  postsettlement = 0.8
)

Animation

Use animate_coralseed() for communication outputs. Keep animation chunks unevaluated in pkgdown unless the output is cached and intentionally committed.

animate_coralseed(
  seed_particles_input = seeded,
  settle_particles_input = settled,
  seascape_probability = seascape,
  output = "outputs/lizard_particle_animation.gif"
)