Nothing
# load needed library
library(raster)
# get path containing example rasters
datapath <- system.file(file.path("extdata", "WorldCenter"), package="gen3sis")
# create raster bricks
temperature_brick <- brick(file.path(datapath, "input_rasters/temp_rasters.grd"))
aridity_brick <- brick(file.path(datapath, "input_rasters/arid_rasters.grd"))
area_brick <- brick(file.path(datapath, "input_rasters/area_rasters.grd"))
# create sub-list of environmental variables for fast example
# (i.e. 4 time-steps)
landscapes_sub_list <- list(temp=NULL, arid=NULL, area=NULL)
for(i in 1:4){
landscapes_sub_list$temp <- c(landscapes_sub_list$temp, temperature_brick[[i]])
landscapes_sub_list$arid <- c(landscapes_sub_list$arid, aridity_brick[[i]])
landscapes_sub_list$area <- c(landscapes_sub_list$area, area_brick[[i]])
}
# define cost function, crossing water as double as land sites
cost_function_water <- function(source, habitable_src, dest, habitable_dest) {
if(!all(habitable_src, habitable_dest)) {
return(2/1000)
} else {
return(1/1000)
}
}
\dontrun{
# create input landscape ready for gen3sis from sub-list
# (i.e. 10 time-steps) and only local-distances.
create_input_landscape(
landscapes = landscapes_sub_list,
cost_function = cost_function_water,
output_directory = file.path(tempdir(), "landscape_sub"),
directions = 8, # surrounding sites for each site
timesteps = paste0(round(150:147,2), "Ma"),
calculate_full_distance_matrices = FALSE) # full distance matrix
# create list of all environmental variables available
landscapes_list <- list(temp=NULL, arid=NULL, area=NULL)
for(i in 1:nlayers(temperature_brick)){
landscapes_list$temp <- c(landscapes_list$temp, temperature_brick[[i]])
landscapes_list$arid <- c(landscapes_list$arid, aridity_brick[[i]])
landscapes_list$area <- c(landscapes_list$area, area_brick[[i]])
}
# create input landscape ready for gen3sis (~ 3min run-time)
# and full distance matrix
create_input_landscape(
landscapes = landscapes_list,
cost_function = cost_function_water,
output_directory = file.path(tempdir(), "landscape_WorldCenter_5"),
directions = 8, # surrounding sites for each site
timesteps = paste0(round(150:100,2), "Ma"),
crs="+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0",
calculate_full_distance_matrices = FALSE) # full distance matrix
}
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