create_input_landscape: create an landscape input from a named list of rasters or...

In gen3sis: General Engine for Eco-Evolutionary Simulations

create an landscape input from a named list of rasters or raster files

Description

create an landscape input from a named list of rasters or raster files

Usage

create_input_landscape(
  landscapes,
  cost_function,
  directions,
  output_directory,
  timesteps = NULL,
  calculate_full_distance_matrices = FALSE,
  crs = NULL,
  overwrite_output = FALSE,
  verbose = FALSE
)

Arguments

landscapes	list of named list(s) of raster(s) or raster file(s) name(s). Starting from the present towards the past. NOTE: the list names are important since these are the environmental names
cost_function	function that returns a cost value between a pair of sites (neighbors) that should have the following signature: cost_function <- function(src, src_habitable, dest, dest_habitable){ rules for environmental factors to be considered (e.g. elevation) return(cost value) } where: **src** is a vector of environmental conditions for the origin sites, **src_habitable** (TRUE or FALSE) for habitable condition of the origin sites, **dest** is a vector of environmental conditions for the destination site, dest_habitable (TRUE or FALSE) for habitable condition of the destination cell
directions	4, 8 or 16 neighbors, dictates the connection of cell neighbors on adjacency matrix (see gistance package)
output_directory	path for storing the gen3sis ready landscape (i.e. landscape.rds, metadata.txt and full- and/or local_distance folders)
timesteps	vector of names for every time-step to represent the time-step at gen3sis ready landscape. If timesteps=NULL (default), time-steps are sequentially numbered from 0 to the latest time-step.
calculate_full_distance_matrices	should a full distance matrix be calculated? TRUE or FALSE? If TRUE calculates the entire distance matrix for every time-step and between all habitable cells (faster CPU time, higher storage required). If FALSE (default), only local distances are calculated (slower CPU time when simulating but smaller gen3sis landscape size)
crs	the coordinate reference system in crs format (see raster::crs)
overwrite_output	TRUE or FALSE
verbose	print distance calculation progress (default: FALSE)

Details

This function creates the input landscapes files needed by the run_simulation function. It uses as input the dynamic landscape rasters and user defined geodesimal corrections as well as rules to define the connection costs between sites

Value

no return object. This function saves the landscape input files for gen3sis at the output_directory

See Also

run_simulation

Examples

# 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)
  }
}

## Not run: 
# 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

## End(Not run)

gen3sis documentation built on Nov. 22, 2023, 5:07 p.m.