metaRangeSimulation {metaRange}R Documentation

metaRangeSimulation object

Description

Creates an simulation object in form of an R6 class that stores and handles all the individual parts that are necessary to run a simulation.

Value

A ⁠<metaRangeSimulation>⁠ object

Public fields

ID

⁠<string>⁠ simulation identification.

globals

⁠<environment>⁠ a place to store global variables.

environment

⁠<metaRangeEnvironment>⁠ A metaRangeEnvironment that holds all the environmental values influencing the simulation.

number_time_steps

⁠<integer>⁠ number of time steps in the simulation.

time_step_layer

⁠<integer>⁠ vector of layer IDs that describe which environmental layer to use at each time step.

current_time_step

⁠<integer>⁠ current time step.

queue

⁠<metaRangePriorityQueue>⁠ manages the order in which the processes should be executed.

processes

⁠<list>⁠ of global (simulation level) ⁠<metaRangeProcess>⁠ (es).

seed

⁠<integer>⁠ seed for the random number generator.

Methods

Public methods

Method new()

Creates a new metaRangeSimulation object.

Usage
metaRangeSimulation$new(source_environment, ID = NULL, seed = NULL)
Arguments
source_environment

⁠<SpatRasterDataset>⁠ created by terra::sds() that represents the environment. The individual data sets represent different environmental variables (e.g. temperature or habitat availability) and the different layer of the data sets represent the different timesteps of the simulation. The function metaRangeSimulation⁠$set_time_layer_mapping()⁠ can be used to extend/ shorten the simulation timesteps and set the mapping between each time step and a corresponding environmental layer. This can be used e.g. to repeat the first (few) layer as a burn-in period. The number of layers must be the same for all data sets.

ID

⁠<string>⁠ optional simulation identification string. Will be set automatically if none is specified.

seed

⁠<integer>⁠ optional seed for the random number generator. Will be set automatically if none is specified.

Returns

A ⁠<metaRangeSimulation>⁠ object.

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim

Method add_globals()

Add global variables to the simulation

Usage
metaRangeSimulation$add_globals(...)
Arguments
...

⁠<any>⁠ the variables to add. Variables to add to the simulation. They will be saved and accessible through the 'globals' field.

Returns

⁠<invisible self>⁠

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_globals(a = 1, b = 2)
sim$globals$a
#> [1] 1

Method set_time_layer_mapping()

Set the time layer of the simulation.

Usage
metaRangeSimulation$set_time_layer_mapping(x)
Arguments
x

⁠<integer>⁠ vector of layer indices that describe which environmental layer to use at each time step.

Returns

⁠<invisible self>⁠

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$set_time_layer_mapping(1:2)
stopifnot(identical(sim$time_step_layer, 1:2))

Method get_current_time_step()

Get current time step

Usage
metaRangeSimulation$get_current_time_step()
Returns

⁠<integer>⁠ the current time step

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$get_current_time_step()
#> [1] 1

Method add_species()

Adds new species to the simulation

Usage
metaRangeSimulation$add_species(names)
Arguments
names

⁠<character>⁠ names of the species to add.

Returns

⁠<invisible boolean>⁠ TRUE on success FALSE on failure.

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species(c("species_1", "species_2"))
sim$species_1

Method species_names()

Returns the names of all species in the simulation.

Usage
metaRangeSimulation$species_names()
Returns

⁠<character>⁠ vector of species names

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_species("species_2")
sim$species_names()
#> [1] "species_1" "species_2"

Method add_process()

Adds a process to the simulation.

Usage
metaRangeSimulation$add_process(
  species = NULL,
  process_name,
  process_fun,
  execution_priority,
  queue = TRUE
)
Arguments
species

⁠<character>⁠ Names of the species that the process should be added to. If NULL the process will be added to the simulation object itself.

process_name

⁠<string>⁠ Name of the process to add.

process_fun

⁠<named function>⁠ The function to call when the process gets executed.

execution_priority

⁠<positive integer>⁠ When this process should run within each time step. 1 == highest priority i.e. this function will be the executed first.

queue

⁠<boolean>⁠ If TRUE the process will be added to the process execution queue directly. If FALSE the process will be added to the simulation but not to the queue, which means that in order to execute the process, it has to be added manually via the metaRangePriorityQueue⁠$enqueue()⁠ method.

Returns

⁠<invisible self>⁠.

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_process("species_1", "species_process_1", function() {message("process_1")}, 1)
sim$species_1$processes$species_process_1
sim$add_process(species = NULL, "global_process_2", function() {message("process_2")}, 2)
sim$processes$global_process_2

Method add_traits()

Adds traits to a species.

Usage
metaRangeSimulation$add_traits(species, population_level = TRUE, ...)
Arguments
species

⁠<character>⁠ Names of the species that the traits should be added to.

population_level

⁠<boolean>⁠ If TRUE the traits will be added at the population level (i.e. as a matrix with same dimensions (nrow/ncol) as the environment with one value for each population). This means that the traits either need to be single values that will be extended to such a matrix via base::matrix() or they already need to be a matrix with these dimension. If FALSE the traits will be added without any conversion and may have any type and dimension.

...

⁠<atomic>⁠ (see base::is.atomic()) The named traits to be added. Named means: Name = value e.g. a = 1.

Returns

⁠<invisible self>⁠.

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_traits("species_1", population_level = TRUE, a = 1)
sim$add_traits("species_1", population_level = FALSE, b = 2, c = "c")
sim$species_1$traits$a
#>      [,1] [,2]
#> [1,]    1    1
#> [2,]    1    1
sim$species_1$traits$b
#> [1] 2
sim$species_1$traits$c
#> [1] "c"

Method exit()

When called, will end the simulation (prematurely) once the current process is finished. Useful to e.g. end the simulation safely (i.e. without an error) when no species is alive anymore and there would be no benefit to continue the execution until the last time step.

Usage
metaRangeSimulation$exit()
Returns

⁠invisible NULL⁠

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
names(sim_env) <- "env_var_name"
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_process("species_1", "species_process_1", function() {self$sim$exit()}, 1)
sim$begin()

Method begin()

Begins the simulation

Usage
metaRangeSimulation$begin()
Returns

⁠<invisible self>⁠ The finished simulation

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
names(sim_env) <- "env_var_name"
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_process(
     species = NULL,
     "timestep_counter",
     function() {
         message("timestep: ", self$get_current_time_step())
     },
     1
)
sim$begin()

Method print()

Prints information about the simulation to the console

Usage
metaRangeSimulation$print()
Returns

⁠<invisible self>⁠

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$print()

Method summary()

Summarizes information about the simulation and outputs it to the console

Usage
metaRangeSimulation$summary()
Returns

⁠<invisible self>⁠

Examples
sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$summary()

Examples


## ------------------------------------------------
## Method `metaRangeSimulation$new`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim

## ------------------------------------------------
## Method `metaRangeSimulation$add_globals`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_globals(a = 1, b = 2)
sim$globals$a
#> [1] 1

## ------------------------------------------------
## Method `metaRangeSimulation$set_time_layer_mapping`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$set_time_layer_mapping(1:2)
stopifnot(identical(sim$time_step_layer, 1:2))

## ------------------------------------------------
## Method `metaRangeSimulation$get_current_time_step`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$get_current_time_step()
#> [1] 1

## ------------------------------------------------
## Method `metaRangeSimulation$add_species`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species(c("species_1", "species_2"))
sim$species_1

## ------------------------------------------------
## Method `metaRangeSimulation$species_names`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_species("species_2")
sim$species_names()
#> [1] "species_1" "species_2"

## ------------------------------------------------
## Method `metaRangeSimulation$add_process`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_process("species_1", "species_process_1", function() {message("process_1")}, 1)
sim$species_1$processes$species_process_1
sim$add_process(species = NULL, "global_process_2", function() {message("process_2")}, 2)
sim$processes$global_process_2

## ------------------------------------------------
## Method `metaRangeSimulation$add_traits`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_traits("species_1", population_level = TRUE, a = 1)
sim$add_traits("species_1", population_level = FALSE, b = 2, c = "c")
sim$species_1$traits$a
#>      [,1] [,2]
#> [1,]    1    1
#> [2,]    1    1
sim$species_1$traits$b
#> [1] 2
sim$species_1$traits$c
#> [1] "c"

## ------------------------------------------------
## Method `metaRangeSimulation$exit`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
names(sim_env) <- "env_var_name"
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_species("species_1")
sim$add_process("species_1", "species_process_1", function() {self$sim$exit()}, 1)
sim$begin()

## ------------------------------------------------
## Method `metaRangeSimulation$begin`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2, nlyr = 4))
names(sim_env) <- "env_var_name"
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$add_process(
     species = NULL,
     "timestep_counter",
     function() {
         message("timestep: ", self$get_current_time_step())
     },
     1
)
sim$begin()

## ------------------------------------------------
## Method `metaRangeSimulation$print`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$print()

## ------------------------------------------------
## Method `metaRangeSimulation$summary`
## ------------------------------------------------

sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))
sim <- metaRangeSimulation$new(source_environment = sim_env)
sim$summary()
[Package metaRange version 1.1.4 Index]