Simulated reseeding event at Mermaid Bay, Lizard Island
1) seed particles
library(coralseed)
library(ggplot2)
library(tidyverse)
library(sf)
library(tmap)
sf_use_s2(FALSE)
# load seascape
lizard_benthic_map <- system.file("extdata", "Lizard_Benthic.geojson", package = "coralseed") |>
st_read(quiet=TRUE)
lizard_reef_map <- system.file("extdata", "Lizard_Geomorphic.geojson", package = "coralseed") |>
st_read(quiet=TRUE)
lizard_seascape <- seascape_probability(reefoutline=lizard_reef_map, habitat=lizard_benthic_map)
# load particles
lizard_particles_sf <- system.file("extdata", "lizard_del_14_1512_sim1_10.json", package = "coralseed") |> st_read(quiet=TRUE)
# run seed particles
lizard_particles <- seed_particles(lizard_particles_sf,
zarr = FALSE,
set.centre = TRUE,
seascape = lizard_seascape,
probability = "additive",
limit.time = 12,
competency.function = "exponential",
crs = 20353,
simulate.mortality = "typeIII",
simulate.mortality.n = 0.1,
return.plot = TRUE,
return.summary = TRUE,
silent = FALSE)2) settle particles
lizard_settlers <- settle_particles(lizard_particles,
probability = "additive",
return.plot=FALSE,
silent = TRUE)
plot_particles(lizard_settlers$points, lizard_seascape)
lizard_settlement_density <- settlement_density(lizard_settlers$points)
lizard_settlement_summary <- settlement_summary(lizard_particles, lizard_settlers, cellsize=50)3) map coralseed
map_coralseed(seed_particles_input = lizard_particles,
settle_particles_input = lizard_settlers,
settlement_density_input = lizard_settlement_density,
seascape_probability = lizard_seascape,
restoration.plot = c(100,100),
show.footprint = TRUE,
show.tracks = TRUE,
subsample = 1000,
webGL = TRUE)4) coralseed outputs
flowchart_coralseed(lizard_particles, lizard_settlers, multiplier=1000, postsettlement=0.8)