Create an spaces input from a named list of rasters or raster files and user defined cost function

Create an spaces input from a named list of rasters or raster files and user defined cost function

Usage

create_spaces_raster(
  raster_list,
  cost_function,
  directions = 16,
  output_directory,
  full_dists = FALSE,
  overwrite_output = FALSE,
  verbose = FALSE,
  duration = list(from = NA, to = NA, by = NA, unit = "Ma"),
  geodynamic = NULL,
  ...
)

Arguments

raster_list

list of named list(s) of raster(s) or raster file(s) name(s). Starting from the past towards the present. 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). This does not control the dispersal processes directly in the simulation, it only makes diagonal distances less biased. E.g., when using directions = 4, diagonals are not directly computed, thus inflating distances for diagonal movement. Default is 16.

output_directory

path for storing the gen3sis ready space (i.e. space.rds, metadata.txt and full- and/or local_distance folders)

full_dists

should a full distance matrix be calculated? TRUE or FALSE? Default is 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 space size)

overwrite_output

TRUE or FALSE

verbose

print distance calculation progress (default: FALSE)

duration

list with from, to, by and unit. Use negative value to represent past, 0 to represent present and positive values to represent future. E.g., a spaces from 10 Ma in the past to 10 Ma into the future, each timestep comprising 5 Ma: duration = list(from = -10, to = 10, by = 5, unit = "Ma")

geodynamic

True or False, if the space is dynamic (e.g. sea-level change) or static. Default is NULL, i.e. deciding final value based on the input data using ?is_geodynamic.

...

additional arguments to be passed to the create_spaces function. Possible arguments include:

• author: author of the space, see ?create_spaces

• source: source of the space, see ?create_spaces

• crs: the coordinate reference system in crs format (see raster::crs). Default is defined by create_spaces

• description: list with env and methods, see ?create_spaces

Value

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

Details

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

See also

run_simulation

Examples

if (FALSE) { # \dontrun{
library(terra)
library(gen3sis2)
# Get some rasters for each timestep
temperature <- terra::rast("your/temperature_raster.tif")
aridity <- terra::rast("your/aridity_raster.tif")
precipitation <- terra::rast("your/precipitation_raster.tif")
  
# Organize them
environmental_variables <- list(
  temperature = temperature,
  aridity = aridity,
  precipitation = precipitation
)
  
create_spaces_raster(
  raster_list = environmental_variables,
  cost_function = function(source, dest) { # any cost function
    if (!all(source$habitable, dest$habitable)) {
      return(2 / 1000)
    } else {
      return(1 / 1000)
    }
  },
  directions = 8,
  output_directory = "./where/to/save",
  full_dists = TRUE, # save full distance matrices
  overwrite_output = TRUE,
  verbose = TRUE,
  duration = list(from = 65, to = 0, by = -1, unit = "Ma"),
  geodynamic = TRUE
)
} # }