Package 'rangr'

Simulating Dispersal

Description

This function simulates dispersal for each grid cell by calculating the number of individuals dispersing out of the cell and the number of individuals dispersing into the cell.

Usage

disp(
  N_t,
  id,
  id_matrix,
  data_table,
  kernel,
  dens_dep,
  dlist,
  id_within,
  within_mask,
  border,
  planar,
  dist_resolution,
  max_dist,
  dist_bin,
  ncells_in_circle,
  cl = NULL
)

Arguments

N_t	integer matrix representing population numbers at a single time step; NA indicates cells outside the study area
id	SpatRaster object (of the same size as N_t) with cell identifiers
id_matrix	id in matrix format
data_table	matrix that contains information about all cells in current time points
kernel	function defining dispersal kernel
dens_dep	character vector of length 1 specifying if the probability of settling in a target grid cell is (case-sensitive, default "K2N"): "none" - fully random, "K" - proportional to the carrying capacity of a target cell, "K2N" - density-dependent, i.e. proportional to the ratio of carrying capacity of a target cell to the number of individuals already present in a target cell
dlist	list with identifiers of target cells at a specified distance from a focal cell
id_within	integer vector with identifiers of cells inside the study area
within_mask	logical matrix that specifies boundaries of the study area
border	character vector of length 1 defining how to deal with borders (case-sensitive, default "absorbing"): "reprising" - cells outside the study area are not allowed as targets for dispersal "absorbing" - individuals that disperse outside the study area are removed from the population
planar	logical vector of length 1; TRUE if input maps are planar rasters, FALSE if input maps are lon/lat rasters
dist_resolution	integer vector of length 1; dimension of one side of one cell of id; in case of an irregular grid or lon/lat raster it is calculated during initialisation
max_dist	distance (in the same units as used in the raster id) specifying the maximum range at which identifiers of target dispersal cells are determined in advance (see initialise)
dist_bin	numeric vector of length 1 with value ⁠>= 0⁠; in case of an irregular grid or lon/lat raster it is calculated during initialisation
ncells_in_circle	numeric vector; number of cells on each distance
cl	if simulation is done in parallel, the name of a cluster object created by makeCluster

Details

The function is used by sim internally and is not intended to be called by the user. The parameters for this function are passed from a sim_data object created by initialise.

Dispersal distance is expressed in original spatial units of the SpatRaster provided to the sim function (n1_map and K_map). However, it is internally converted to units of the simulation (i.e. the size of a single cell) by calculating round(distance/resolution). If the selected dispersal distance is smaller than resolution/2, the individual does not disperse effectively and remains in the same cell. The dispersal rate (proportion of dispersing individuals) can be estimated from the dispersal kernel probability function by calculating the probability that the dispersal distance is greater than resolution/2.

Value

The function returns a list that contains two matrices:

em - emigration matrix with the number of individuals that dispersed from each cell

im - immigration matrix with the number of individuals that dispersed to each cell

Examples

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

# disp
disp_output <- disp(
  N_t = sim_data$n1_map,
  id = unwrap(sim_data$id),
  id_matrix = as.matrix(unwrap(sim_data$id), wide = TRUE),
  data_table = sim_data$data_table,
  kernel = sim_data$kernel,
  dens_dep = sim_data$dens_dep,
  dlist = sim_data$dlist,
  id_within = sim_data$id_within,
  within_mask = sim_data$within_mask,
  border = sim_data$border,
  planar = sim_data$planar,
  dist_resolution = sim_data$dist_resolution,
  max_dist = sim_data$max_dist,
  dist_bin = sim_data$dist_bin,
  ncells_in_circle = sim_data$ncells_in_circle
)

# immigration and emigration matrices
names(disp_output)

---

Observation Process

Description

This function simulates an observation process. It accepts the sim_results object, which is generated by the sim function, and applies the virtual ecologist approach on the N_map component of the object. The function returns a data.frame with the 'observed' abundances.

Usage

get_observations(
  sim_data,
  sim_results,
  type = c("random_one_layer", "random_all_layers", "from_data", "monitoring_based"),
  obs_error = c("rlnorm", "rbinom"),
  obs_error_param = NULL,
  ...
)

Arguments

sim_data	sim_data object from initialise containing simulation parameters
sim_results	sim_results object; returned by sim function
type	character vector of length 1; describes the sampling type (case-sensitive): "random_one_layer" - random selection of cells for which abundances are sampled; the same set of selected cells is used across all time steps. "random_all_layers" - random selection of cells for which abundances are sampled; a new set of cells is selected for each time step. "from_data" - user-defined selection of cells for which abundances are sampled; the user is required to provide a data.frame containing three columns: "x", "y" and "time_step". "monitoring_based" - user-defined selection of cells for which abundances are sampled; the user is required to provide a matrix object with two columns: "x" and "y"; the abundance from given cell is sampled by different virtual observers in different time steps; a geometric distribution (rgeom) is employed to define whether a survey will be conducted by the same observer for several years or not conducted at all.
obs_error	character vector of length 1; type of the distribution that defines the observation process: "rlnorm" (the log normal distribution) or "rbinom" (the binomial distribution)
obs_error_param	numeric vector of length 1; standard deviation (on a log scale) of the random noise in observation process generated from the log-normal distribution (rlnorm) or probability of detection (success) when the binomial distribution ("rbinom") is used.
...	other necessary internal parameters: prop numeric vector of length 1; proportion of cells to be sampled (default prop = 0.1); used when ⁠type = "random_one_layer" or "random_all_layers"⁠, points data.frame or matrix with 3 numeric columns named "x", "y", and "time_step" containing coordinates and time steps from which observations should be obtained; used when type = "from_data", cells_coords data.frame or matrix with 2 columns named "x" and "y"; survey plots coordinates; used when type = "monitoring_based" prob numeric vector of length 1; a parameter defining the shape of rgeom distribution; defines whether an observation will be made by the same observer for several years, and whether it will not be made at all (default prob = 0.3); used when type = "monitoring_based" progress_bar logical vector of length 1; determines if a progress bar for observation process should be displayed (default progress_bar = FALSE); used when type = "monitoring_based"

Value

data.frame object with geographic coordinates, time steps, estimated abundance, observation error (if obs_error_param is provided), and observer identifiers (if type = "monitoring_based"). If type = "from_data", returned object is sorted in the same order as the input points.

Examples

## Not run: 

library(terra)
n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

# prepare data
sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

sim_1 <- sim(obj = sim_data, time = 110, burn = 10)

# 1. random_one_layer
sample1 <- get_observations(
  sim_data,
  sim_1,
  type = "random_one_layer",
  prop = 0.1
)

# 2. random_all_layers
sample2 <- get_observations(
  sim_data,
  sim_1,
  type = "random_all_layers",
  prop = 0.15
)

# 3. from_data
sample3 <- get_observations(
  sim_data,
  sim_1,
  type = "from_data",
  points = observations_points
)

# 4. monitoring_based
# define observations sites
all_points <- xyFromCell(unwrap(sim_data$id), cells(unwrap(sim_data$K_map)))
sample_idx <- sample(1:nrow(all_points), size = 20)
sample_points <- all_points[sample_idx, ]

sample4 <- get_observations(
  sim_data,
  sim_1,
  type = "monitoring_based",
  cells_coords = sample_points,
  prob = 0.3,
  progress_bar = TRUE
)

# 5. noise "rlnorm"
sample5 <- get_observations(sim_data,
  sim_1,
  type = "random_one_layer",
  obs_error = "rlnorm",
  obs_error_param = log(1.2)
)

# 6. noise "rbinom"
sample6 <- get_observations(sim_data,
  sim_1,
  type = "random_one_layer",
  obs_error = "rbinom",
  obs_error_param = 0.8
)


## End(Not run)

---

Population Growth Functions

Description

Population growth functions are used during simulation conducted by the sim function. The user is required to specify the name of a growth function while initialising the sim_data object using initialise.

Usage

exponential(x, r, ...)

ricker(x, r, K, A = NA)

gompertz(x, r, K, A = NA)

Arguments

x	number of individuals
r	intrinsic population growth rate
...	not used, added for compatibility reasons
K	carrying capacity
A	coefficient of Allee effect (A <= 0: weak, A > 0: strong, NA: none)

Details

x can be a vector, matrix, SpatRaster or any other R object for which basic arithmetic operations produce valid results. These functions are intended to be used in the sim function, where x is a matrix of the same dimensions as the SpatRaster object specified in n1_map parameter.

Value

Object of the same dimensions as x that contains expected number of individuals in the next time step.

References

Boukal, D. S., & Berec, L. (2002). Single-species models of the Allee effect: extinction boundaries, sex ratios and mate encounters. Journal of Theoretical Biology, 218(3), 375-394. doi:10.1006/jtbi.2002.3084

Gompertz, B. (1825) On the Nature of the Function Expressive of the Law of Human Mortality, and on a New Mode of Determining the Value of Life Contigencies. Philosophical Transactions of the Royal Society of London, 115, 513-583. doi:10.1098/rstl.1825.0026

Ricker, W.E. (1954) Stock and Recruitment. Journal of the Fisheries Research Board of Canada, 11, 559-623. doi:10.1139/f54-039

Hostetler, J.A. and Chandler, R.B. (2015), Improved state-space models for inference about spatial and temporal variation in abundance from count data. Ecology, 96: 1713-1723. doi:10.1890/14-1487.1

Courchamp, F., L. Berec and J. Gascoigne. 2008. Allee Effects in Ecology and Conservation. Oxford University Press, New York. 256 pp. ISBN 978-0-19-857030-1

Examples

x <- 1:10
exponential(x, r = 0.4)

ricker(x, r = 2, K = 5)
ricker(x, r = 2, K = 5, A = -5)

gompertz(x, r = 1.2, K = 5)
gompertz(x, r = 1.2, K = 5, A = 5)

---

Prepare Data Required To Perform A Simulation

Description

This function generates a sim_data object containing all the necessary information required to run a simulation by the sim function. The input maps (n1_map and K_map) can be in the Cartesian or longitude/latitude coordinate system.

Usage

initialise(
  n1_map,
  K_map,
  K_sd = 0,
  r,
  r_sd = 0,
  growth = "gompertz",
  A = NA,
  dens_dep = c("K2N", "K", "none"),
  border = c("reprising", "absorbing"),
  kernel_fun = "rexp",
  ...,
  max_dist = NA,
  calculate_dist = TRUE,
  dlist = NULL,
  progress_bar = TRUE,
  quiet = FALSE
)

Arguments

n1_map	SpatRaster object with one layer; population numbers in every grid cell at the first time step
K_map	SpatRaster object with one layer; carrying capacity map (if K is constant across time) or maps (if K is time-varying)
K_sd	numeric vector of length 1 with value ⁠>= 0⁠ (default 0); this parameter can be used if additional environmental stochasticity is required; if K_sd > 0, random numbers are generated from a log-normal distribution with the mean K_map and standard deviation K_sd
r	numeric vector of length 1; intrinsic population growth rate
r_sd	numeric vector of length 1 with value ⁠>= 0⁠ (default 0); if additional demographic stochasticity is required, r_sd > 0 is the standard deviation for a normal distribution around r (defined for each time step)
growth	character vector of length 1; the name of a population growth function, either defined in growth or provided by the user (case-sensitive, default "gompertz")
A	numeric vector of length 1; strength of the Allee effect (see the growth function)
dens_dep	character vector of length 1 specifying if the probability of settling in a target grid cell is (case-sensitive, default "K2N"): "none" - fully random, "K" - proportional to the carrying capacity of a target cell, "K2N" - density-dependent, i.e. proportional to the ratio of carrying capacity of a target cell to the number of individuals already present in a target cell
border	character vector of length 1 defining how to deal with borders (case-sensitive, default "absorbing"): "reprising" - cells outside the study area are not allowed as targets for dispersal "absorbing" - individuals that disperse outside the study area are removed from the population
kernel_fun	character vector of length 1; name of a random number generation function defining a dispersal kernel (case-sensitive, default "rexp")
...	any parameters required by kernel_fun
max_dist	numeric vector of length 1; maximum distance of dispersal to pre-calculate target cells
calculate_dist	logical vector of length 1; determines if target cells will be precalculated
dlist	list; target cells at a specified distance calculated for every cell within the study area
progress_bar	logical vector of length 1; determines if progress bar for calculating distances should be displayed
quiet	logical vector of length 1; determines if messages should be displayed

Details

The most time-consuming part of computations performed by the sim function is the simulation of dispersal. To speed it up, a list containing indexes of target cells at a specified distance from a focal cell is calculated in advance and stored in a dlist slot. The max_dist parameter sets the maximum distance at which this pre-calculation is performed. If max_dist is NULL, it is set to 0.99 quantile from the kernel_fun. All distance calculations are always based on metres if the input maps are latitude/longitude. For planar input maps, distances are calculated in map units, which are typically metres, but check the crs() if in doubt.

If the input maps are in the Cartesian coordinate system and the grid cells are squares, then the distances between cells are calculated using the distance function from the terra package. These distances are later divided by the resolution of the input maps.

For input maps with grid cells in shapes other than squares (e.g. with rectangular cells or longitude/latitude coordinate system), the distance resolution is calculated by finding the shortest distance between each "queen" type neighbor. All distances calculated by the distance function are further divided by this distance resolution. To avoid discontinuities in the distances at which the target cells are located, an additional parameter dist_bin is calculated as half of the maximum distance between each "queen" type neighbour. It is used to expand the distances at which target cells are located from a single number to a range.

NA in the input maps represents cells outside the study area.

The K_get_interpolation function can be used to prepare K_map that changes over time. This may be useful, when simulating environmental change or exploring the effects of ecological disturbances.

Value

Object of class sim_data which inherits from list. This object contains all necessary information to perform a simulation using sim function.

References

Hijmans R (2024). terra: Spatial Data Analysis. R package version 1.7-81, https://rspatial.github.io/terra/, https://rspatial.org/

Solymos P, Zawadzki Z (2023). pbapply: Adding Progress Bar to '*apply' Functions. R package version 1.7-2, https://CRAN.R-project.org/package=pbapply.

See Also

update

Examples

## Not run: 

# input maps
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))
K_small_changing <- rast(system.file("input_maps/K_small_changing.tif",
                         package = "rangr"))
n1_small_lon_lat <- rast(system.file("input_maps/n1_small_lon_lat.tif", package = "rangr"))
K_small_lon_lat <- rast(system.file("input_maps/K_small_lon_lat.tif", package = "rangr"))

# basic example
sim_data_1 <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

# example with changing environment
K_interpolated <- K_get_interpolation(
  K_small_changing,
  K_time_points = c(1, 25, 50)
)

sim_data_2 <- initialise(
  n1_map = n1_small,
  K_map = K_interpolated,
  r = log(2),
  rate = 1 / 1e3
)

# example with lon/lat rasters
sim_data_3 <- initialise(
  n1_map = n1_small_lon_lat,
  K_map = K_small_lon_lat,
  r = log(2),
  rate = 1 / 1e3
)

# example without progress bar and messages
sim_data_4 <- initialise(
  n1_map = n1_small, K_map = K_small, K_sd = 0.1, r = log(5),
  r_sd = 4, growth = "ricker", rate = 1 / 200,
  max_dist = 5000, dens_dep = "K2N", progress_bar = FALSE, quiet = TRUE
)

## End(Not run)

---

Example Of Carrying Capacity Map (Big)

Description

SpatRaster object representing a carrying capacity map projected to WGS 84 (CRS84) from the original raster K_big. This map can be used as a carrying capacity map to initialise data necessary to perform a simulation with the sim function. It is compatible with the n1_big_lon_lat.tif raster.

Format

SpatRaster object with 74 rows and 125 columns containing integer values 0-25 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_big_lon_lat.tif", package = "rangr")

---

Example Of Carrying Capacity Map (Big)

Description

SpatRaster object that can be used as a carrying capacity map to initialise data necessary to perform a simulation with the sim function. This map is compatible with n1_big.tif.

Format

SpatRaster object with 100 rows and 100 columns containing integer values 0-25 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_big.tif", package = "rangr")

---

Prepare Time-Varying Carrying Capacity Maps

Description

This function linearly interpolates values in a series of carrying capacity maps.

Usage

K_get_interpolation(K_map, K_time_points = NULL, time = NULL)

Arguments

K_map	SpatRaster object with carrying capacity maps for each K_time_points
K_time_points	integer vector; time for each layer in K_map, should contain unique values
time	integer vector of length 1; number of total time steps required (this is defined when evoking the function sim).

Details

To simulate dynamic environmental scenarios (e.g. climate change, land use change, ecological disturbance, etc.) one needs to provide time-varying carrying capacity maps.

Either K_time_points or the time parameter is needed to perform interpolation. If the interpolation should be calculated between two carrying capacity maps, there is no need to pass the time points, because 1 will be set as the starting time point and time will be used as the ending point. On the other hand, in the absence of the time argument, the maximum element of K_time_points is considered to be the ending point for the interpolation.

Value

SpatRaster object with number of layers equal to time.

Examples

## Not run: 

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small_changing <- rast(system.file("input_maps/K_small_changing.tif",
package = "rangr"))

K_interpolated_01 <- K_get_interpolation(
  K_small_changing,
  K_time_points = c(1, 10, 15)
)

K_two_layers <- subset(
  K_small_changing,
  c(1, 2)
)
K_interpolated_02 <- K_get_interpolation(
  K_two_layers,
  time = 15
)


## End(Not run)

---

Example Of Changing Carrying Capacity Maps (Small)

Description

SpatRaster object representing changing carrying capacity maps projected to WGS 84 (CRS84) from the original raster K_small_changing. These maps can be used as carrying capacity maps to initialise data necessary to perform a simulation with the sim function. To utilise these maps in initialise the user must first use K_get_interpolation to generate a map for every time step of the simulation. These maps are compatible with the n1_small_lon_lat.tif raster.

Format

SpatRaster object with 3 layers, each having 12 rows and 14 columns containing integer values 0-170 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_small_changing_lon_lat.tif", package = "rangr")

---

Example Of Changing Carrying Capacity Maps (Small)

Description

SpatRaster object that can be used as carrying capacity maps to initialise data necessary to perform a simulation with the sim function. To utilise these maps in initialise the user first must use K_get_interpolation to generate a map for every time step of the simulation. These maps are compatible with n1_small.tif. Each subsequent map contains a virtual environment with greater carrying capacity than the previous one.

Format

SpatRaster object with 3 layers, each has 15 rows and 10 columns containing integer values 0-170 and NA's that indicates unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_small_changing.tif", package = "rangr")

---

Example Of Carrying Capacity Map (Small)

Description

SpatRaster object that represents a carrying capacity map projected to WGS 84 (CRS84) from the original raster K_small. This map can be used as a carrying capacity map to initialise data necessary to perform a simulation with the sim function. It is compatible with the n1_small_lon_lat.tif raster.

Format

SpatRaster object with 12 rows and 14 columns containing integer values 0-100 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_small_lon_lat.tif", package = "rangr")

---

Example Of Carrying Capacity Map (Small)

Description

SpatRaster object that can be used a carrying capacity map to initialise data necessary to perform a simulation with the sim function. This map is compatible with n1_small.tif.

Format

SpatRaster object with 15 rows and 10 columns containing integer values 0-100 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example (using spatial autocorrelation).

Examples

system.file("input_maps/K_small.tif", package = "rangr")

---

Example Of Abundance Map At First Time Step Of The Simulation (Big)

Description

SpatRaster object representing an abundance map at the first time step of the simulation projected to WGS 84 (CRS84) from the original raster n1_big. This map can be used as a simulation starting point to initialise data necessary to perform a simulation with the sim function. It is compatible with the K_big_lon_lat.tif map.

Format

SpatRaster object with 74 rows and 125 columns containing integer values 0-50 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example.

Examples

system.file("input_maps/n1_big_lon_lat.tif", package = "rangr")

---

Example Of Abundance Map At First Time Step Of The Simulation (Big)

Description

SpatRaster object that can be used a as simulation starting point to initialise data necessary to perform a simulation with the sim function. This map is compatible with K_big.tif map.

Format

SpatRaster object with 100 rows and 100 columns containing integer values 0-50 and NA's that indicates unsuitable areas.

Source

Data generated in-house to serve as an example.

Examples

system.file("input_maps/n1_big.tif", package = "rangr")

---

Example Of Abundance Map At First Time Step Of The Simulation (Small)

Description

SpatRaster object representing an abundance map at the first time step of the simulation projected to WGS 84 (CRS84) from the original raster n1_small. This map can be used as a simulation starting point to initialise data necessary to perform a simulation with the sim function. It is compatible with the K_small_lon_lat.tif and K_small_changing_lon_lat.tif maps.

Format

SpatRaster object with 12 rows and 14 columns containing integer values 0-10 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example.

Examples

system.file("input_maps/n1_small_lon_lat.tif", package = "rangr")

---

Example Of Abundance Map At First Time Step Of The Simulation (Small)

Description

SpatRaster object that can be used a as simulation starting point to initialise data necessary to perform a simulation with the sim function. This map is compatible with K_small.tif and K_small_changing.tif maps.

Format

SpatRaster object with 15 rows and 10 columns containing integer values 0-10 and NA's indicating unsuitable areas.

Source

Data generated in-house to serve as an example.

Examples

system.file("input_maps/n1_small.tif", package = "rangr")

---

Example Of Observation Points List

Description

A data.frame containing a sample input data to the function get_observations when type argument is set to "from_file". This data is compatible with n1_small.tif, K_small.tif and K_small_changing.tif maps.

Usage

observations_points

Format

A data frame with 1500 rows and 3 variables:

x

x coordinate

y

y coordinate

time_step

time_step at which the abundances should be observed

Source

Data generated in-house to serve as an example

---

Plot sim_results Object

Description

Plots abundances obtained during simulation.

Usage

## S3 method for class 'sim_results'
plot(x, template = NULL, time_points = NULL, range, type, ...)

Arguments

x	sim_results object; returned by sim
template	SpatRaster object; can be used as a template to create returned object
time_points	numeric vector; specifies points in time from which plots will be generated
range	numeric vector of length 2; range of values to be used for the legend (if type = "continuous"), which by default is calculated from the N_map slot of sim_result object
type	character vector of length 1; type of map: "continuous" (default), "classes" or "interval" (case-sensitive)
...	further arguments passed to terra::plot

Value

SpatRaster object with as many layers as the length of time_points parameter

Examples

## Not run: 
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
sim_res <- sim(sim_data, time = 10)
plot(sim_res)
plot(sim_res, template = n1_small, time_points = c(1, 10))

# plot specific area
plot(sim_res, xlim = c(4, 10), ylim = c(0, 10))
plot(sim_res, ext = c(4, 10, 0, 10))
plot(sim_res, template = n1_small, ext = c(274000, 280000, 610000, 620000))

## End(Not run)

---

Print sim_data Object

Description

Print sim_data Object

Usage

## S3 method for class 'sim_data'
print(x, ...)

Arguments

x	sim_data object; returned by the initialise function
...	further arguments passed to or from other methods; currently none specified

Value

sim_data object is invisibly returned (the x param)

Examples

library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
print(sim_data)

---

Print sim_results Object

Description

Print sim_results Object

Usage

## S3 method for class 'sim_results'
print(x, ...)

Arguments

x	sim_results object; returned by the sim function
...	further arguments passed to or from other methods; none specified

Value

sim_results object is invisibly returned (the x param)

Examples

## Not run: 
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
sim_res <- sim(obj = sim_data, time = 20, burn = 5)
print(sim_res)

## End(Not run)

---

Print summary.sim_data Object

Description

Print summary.sim_data Object

Usage

## S3 method for class 'summary.sim_data'
print(x, ...)

Arguments

x	summary.sim_data object; returned by summary.sim_data function
...	further arguments passed to or from other methods; currently none specified

Value

None

Examples

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
summary_sim_data <- summary(sim_data)
print(summary_sim_data)

---

Print summary.sim_results Object

Description

Print summary.sim_results Object

Usage

## S3 method for class 'summary.sim_results'
print(x, ...)

Arguments

x	summary.sim_results object; returned by summary.sim_results function
...	further arguments passed to or from other methods; currently none specified

Value

None

Examples

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
sim_results <- sim(sim_data, time = 10)
summary_sim_results <- summary(sim_results)
print(summary_sim_results)

---

Mechanistic Metapopulation Simulator

Description

This function simulates population growth and dispersal providing a given environmental scenario. All parameters for the simulation must be set in advance using initialise.

Usage

sim(
  obj,
  time,
  burn = 0,
  return_mu = FALSE,
  cl = NULL,
  progress_bar = TRUE,
  quiet = FALSE
)

Arguments

obj	sim_data object created by initialise containing all simulation parameters and necessary data
time	positive integer vector of length 1; number of time steps simulated
burn	positive integer vector of length 1; the number of burn-in time steps that are discarded from the output
return_mu	logical vector of length 1; if TRUE demographic process return expected values; if FALSE the rpois function should be used
cl	an optional cluster object created by makeCluster needed for parallel calculations
progress_bar	logical vector of length 1 determines if progress bar for simulation should be displayed
quiet	logical vector of length 1; determines if warnings should be displayed

Details

This is the main simulation module. It takes the sim_data object prepared by initialise and runs simulation for a given number of time steps. The initial (specified by the burn parameter) time steps are skipped and discarded from the output. Computations can be done in parallel if the name of a cluster created by makeCluster is provided.

Generally, at each time step, simulation consists of two phases: local dynamics and dispersal.

Local dynamics (which connects habitat patches in time) is defined by the function growth. This parameter is specified while creating the obj using initialise, but can be later modified by using the update function. Population growth can be either exponential or density-dependent, and the regulation is implemented by the use of Gompertz or Ricker models (with a possibility of providing any other, user defined function). For every cell, the expected population density during the next time step is calculated from the corresponding number of individuals currently present in this cell, and the actual number of individuals is set by drawing a random number from the Poisson distribution using this expected value. This procedure introduces a realistic randomness, however additional levels of random variability can be incorporated by providing parameters of both demographic and environmental stochasticity while specifying the sim_data object using the initialise function (parameters r_sd and K_sd, respectively).

To simulate dispersal (which connects habitat patches in space), for each individual in a given cell, a dispersal distance is randomly drawn from the dispersal kernel density function. Then, each individual is translocated to a randomly chosen cell at this distance apart from the current location. For more details, see the disp function.

Value

This function returns an object of class sim_results which is a list containing the following components:

• extinction - TRUE if population is extinct or FALSE otherwise

• simulated_time - number of simulated time steps without the burn-in ones

• N_map - 3-dimensional array representing spatio-temporal variability in population numbers. The first two dimensions correspond to the spatial aspect of the output and the third dimension represents time.

In case of a total extinction, a simulation is stopped before reaching the specified number of time steps. If the population died out before reaching the burn threshold, then nothing can be returned and an error occurs.

References

Solymos P, Zawadzki Z (2023). pbapply: Adding Progress Bar to '*apply' Functions. R package version 1.7-2, https://CRAN.R-project.org/package=pbapply.

See Also

get_observations

Examples

## Not run: 

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

# simulation
sim_1 <- sim(obj = sim_data, time = 20)

# simulation with burned time steps
sim_2 <- sim(obj = sim_data, time = 20, burn = 10)

# example with parallelization
library(parallel)
cl <- makeCluster(detectCores())

# parallelized simulation
sim_3 <- sim(obj = sim_data, time = 20, cl = cl)
stopCluster(cl)


# visualisation
plot(
  sim_1,
  time_points = 20,
  template = sim_data$K_map
)

plot(
  sim_1,
  time_points = c(1, 5, 10, 20),
  template = sim_data$K_map
)

plot(
  sim_1,
  template = sim_data$K_map
)


## End(Not run)

---

Subset of Given Time Points from sim_results Object

Description

This function creates a subset of given time points from the sim_results object.

Usage

## S3 method for class 'sim_results'
subset(x, from = NULL, time_points = NULL, ...)

Arguments

x	sim_results object; returned by the sim function
from	numeric vector of length 1; indicates the starting time point from which all time point should be kept
time_points	numeric vector; indicates all time points to keep
...	further arguments to be passed to or from other methods

Details

Either from or time_points argument has to be specified. Time point passed by the from argument will be set as a cutoff point and all abundances for previous time points will be discarded.

Value

sim_results object with only selected time_points present in the N_map slot

Examples

## Not run: 
# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n = n1_small,
  r = log(2),
  K_map = K_small,
  max_dist = 1000,
  rate = 1 / 1e3
)

sim_results <- sim(sim_data, time = 10)
summary(sim_results)

sim_results_cropped <- subset(sim_results, time_points = c(1:2))
summary(sim_results_cropped)

## End(Not run)

---

Summary Of sim_data Object

Description

Summary Of sim_data Object

Usage

## S3 method for class 'sim_data'
summary(object, ...)

Arguments

object	sim_data object; returned by initialise function
...	further arguments passed to or from other methods; currently none specified

Value

summary.sim_data object

Examples

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
summary(sim_data)

---

Summary Of sim_results Object

Description

Summary Of sim_results Object

Usage

## S3 method for class 'sim_results'
summary(object, ...)

Arguments

object	sim_results object; returned by sim function
...	further arguments passed to or from other methods; none specified

Value

summary.sim_results object

Examples

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

# simulation
sim_results <- sim(sim_data, time = 10)
summary(sim_results)

---

Transformation sim_results To Raster

Description

This function transforms selected subset of abundance matrices from sim_results into SpatRaster object. Layers are specified by time_points, which can be one or multiple points in time.

Usage

to_rast(sim_results, time_points = sim_results$simulated_time, template = NULL)

Arguments

sim_results	sim_results object created by sim
time_points	numeric vector of length 1 or more; specifies points in time from which SpatRaster will be created - as default the last year of simulation; if length(time_points) > 0 SpatRaster will be returned with layers for each element of time_points
template	SpatRaster object; can be used as a template to create returned object

Value

SpatRaster based on sim_results object with layers corresponding to time_points.

References

Hijmans R (2024). terra: Spatial Data Analysis. R package version 1.7-81, https://rspatial.github.io/terra/, https://rspatial.org/

Examples

## Not run: 

# data preparation
library(terra)

n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)

# simulation
sim_1 <- sim(obj = sim_data, time = 100)

# raster construction
my_rast <- to_rast(
  sim_1,
  time_points = c(1, 10, 20, 100),
  template = sim_data$K_map
)

# visualization
plot(my_rast, range = range(sim_1$N_map, na.rm = TRUE))


## End(Not run)

---

Update sim_data Object

Description

This function updates a sim_data object.

Usage

## S3 method for class 'sim_data'
update(object, ..., evaluate = TRUE)

Arguments

object	sim_data object; returned by initialise function
...	further arguments passed to or from other methods; currently none specified
evaluate	logical vector of length 1; if TRUE evaluates the new call, otherwise returns the call

Value

If evaluate = TRUE then the updated sim_data object, otherwise the updated call.

Examples

## Not run: 

# data preparation
library(terra)
n1_small <- rast(system.file("input_maps/n1_small.tif", package = "rangr"))
K_small <- rast(system.file("input_maps/K_small.tif", package = "rangr"))

sim_data_1 <- initialise(
  n1_map = n1_small,
  K_map = K_small,
  r = log(2),
  rate = 1 / 1e3
)
summary(sim_data_1)

sim_data_2 <- update(sim_data_1, max_dist = 3000)
summary(sim_data_2)


## End(Not run)

---