Synthos

Installation

git clone git@github.com:open-AIMS/synthos.git .

Example use

The following describe how to use some of the wrapper functions to generate synthetic fixed photo-transect and quadrats data.

Create synthetic reef landscape

library(sf)
library(stars)
library(gstat)
library(INLA)
library(synthos)
config <- list(
  seed = 1,
  crs = 4326,
  model = "Exp",
  psill = 1,
  range = 15,
  nugget = 0,
  alpha = 2,
  kappa = 1,
  variance = 1,
  patch_threshold = 1.75,
  reef_width = 0.01,
  years = 1:12,
  dhw_weight = 0.5,
  cyc_weight = 0.4,
  other_weight = 0.1,
  hcc_growth = 0.3,
  sc_growth =  0.3
)
spatial_domain <- st_geometry(
  st_multipoint(
    x = rbind(
      c(0, -10),
      c(3, -10),
      c(10, -20),
      c(1, -21),
      c(2, -16),
      c(0, -10)
    )
  )
) |>
  st_set_crs(config$crs) |>
  st_cast("POLYGON")
set.seed(config$seed)
spatial_grid <- spatial_domain |>
  st_set_crs(NA) |>
  st_sample(size = 10000, type = "regular") |>
  st_set_crs(config$crs)
sf_use_s2(FALSE)
benthos_reefs_pts <- create_synthetic_reef_landscape(spatial_grid, config)

Generate large scale fixed design

config <- list(n_locs = 25, n_sites = 2, seed = 123)
benthos_fixed_locs_sf <- sampling_design_large_scale_fixed(benthos_reefs_pts, config)

Generate fine scale fixed design

config <- list(
  years =  1:12,
  Number_of_transects_per_site = 5,
  Depths = 2,
  Number_of_frames_per_transect = 100,
  Points_per_frame = 5,
  ## Note, the following are on the link scale
  hcc_site_sigma = 0.5, # variability in Sites within Locations
  hcc_transect_sigma = 0.2, # variability in Transects within Sites
  hcc_sigma = 0.1, # random noise

  sc_site_sigma = 0.05, # variability in Sites within Locations
  sc_transect_sigma = 0.02, # variability in Transects within Sites
  sc_sigma = 0.01, # random noise

  ma_site_sigma = 0.5, # variability in Sites within Locations
  ma_transect_sigma = 0.2, # variability in Transects within Sites
  ma_sigma = 0.1 # random noise
)

benthos_fixed_locs_obs <- sampling_design_fine_scale_fixed(benthos_fixed_locs_sf, config)

Generate photo-transect like data and prepare for reefCloud

config <- list(
  Depths = 2,
  Depth_effect_multiplier = 2,
  Number_of_transects_per_site = 5,
  Number_of_frames_per_transect = 100,
  Points_per_frame = 5
)
benthos_fixed_locs_points <- sampling_design_fine_scale_points(benthos_fixed_locs_obs, config)

reefcloud_synthetic_fixed_benthos <- prepare_for_reefcloud(benthos_fixed_locs_points)

Generate quadrat-like (percent cover) data and prepare for reefCloud

config <- list(
  Depths = 2,
  Depth_effect_multiplier = 2,
  Number_of_transects_per_site = 5,
  Number_of_quadrats_per_transect = 10,
  Quad_sigma = 0.5
)
benthos_fixed_locs_cover <- sampling_design_fine_scale_cover(benthos_fixed_locs_obs, config)

reefcloud_synthetic_fixed_benthos_cover <- prepare_for_reefcloud(benthos_fixed_locs_cover)