Package 'NLMR' reference manual

Title:	Simulating Neutral Landscape Models
Description:	Provides neutral landscape models (<doi:10.1007/BF02275262>, <http://sci-hub.tw/10.1007/bf02275262>). Neutral landscape models range from "hard" neutral models (completely random distributed), to "soft" neutral models (definable spatial characteristics) and generate landscape patterns that are independent of ecological processes. Thus, these patterns can be used as null models in landscape ecology. 'NLMR' combines a large number of algorithms from other published software for simulating neutral landscapes. The simulation results are obtained in a spatial data format (raster* objects from the 'raster' package) and can, therefore, be used in any sort of raster data operation that is performed with standard observation data.
Authors:	Marco Sciaini [aut, cre] , Matthias Fritsch [aut], Maximilian Hesselbarth [aut], Craig Simpkins [aut] , Cédric Scherer [aut] , Sebastian Hanß [aut] , Laura Graham [rev] (Laura reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/188), Jeffrey Hollister [rev] (Jeffrey reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/188)
Maintainer:	Marco Sciaini <[email protected]>
License:	GPL-3
Version:	1.1.1
Built:	2024-09-02 10:18:54 UTC
Source:	https://github.com/ropensci/NLMR

nlm_curds

Description

Simulates a random curd neutral landscape model with optional wheys.

Usage

nlm_curds(curds, recursion_steps, wheyes = NULL, resolution = 1)
nlm_curds(curds, recursion_steps, wheyes = NULL, resolution = 1)

Arguments

`curds`	[`numerical(x)`] Vector with percentage/s to fill with curds (fill with habitat (value == TRUE)).
`recursion_steps`	[`numerical(x)`] Vector of successive cutting steps for the blocks (split 1 block into `x` blocks).
`wheyes`	[`numerical(x)`] Vector with percentage/s to fill with wheys, which fill matrix in an additional step with habitat.
`resolution`	[`numerical(1)`] Resolution of the resulting raster.

Details

Random curdling recursively subdivides the plane into blocks. At each level of the recursion, a fraction of the blocks are declared as habitat (value == TRUE) while the remaining blocks continue to be defined as matrix (value == FALSE) and enter the next recursive cycle.

The optional argument (wheyes) allows wheys to be added, in which a set proportion of cells that were declared matrix (value == FALSE) during recursion, are now set as habitat cells (value == TRUE).

$curds_{1} = curds_{2} = recursion_steps_{2} = ... = curds_{n} = recursion_steps_{n}$

the models resembles a binary random map.

Note that you can not set ncol and nrow with this landscape algorithm. The amount of cells and hence dimension of the raster is given by the vector product of the recursive steps.

Value

raster

References

Keitt TH. 2000. Spectral representation of neutral landscapes. Landscape Ecology 15:479-493.

Szaro, Robert C., and David W. Johnston, eds. Biodiversity in managed landscapes: theory and practice. Oxford University Press, USA, 1996.

Examples


# simulate random curdling
(random_curdling <- nlm_curds(curds = c(0.5, 0.3, 0.6),
                              recursion_steps = c(32, 6, 2)))

# simulate wheyed curdling
(wheyed_curdling <- nlm_curds(curds = c(0.5, 0.3, 0.6),
                              recursion_steps = c(32, 6, 2),
                              wheyes = c(0.1, 0.05, 0.2)))
## Not run: 
# Visualize the NLMs
landscapetools::show_landscape(random_curdling)
landscapetools::show_landscape(wheyed_curdling)

## End(Not run)

# simulate random curdling
(random_curdling <- nlm_curds(curds = c(0.5, 0.3, 0.6),
                              recursion_steps = c(32, 6, 2)))

# simulate wheyed curdling
(wheyed_curdling <- nlm_curds(curds = c(0.5, 0.3, 0.6),
                              recursion_steps = c(32, 6, 2),
                              wheyes = c(0.1, 0.05, 0.2)))
## Not run: 
# Visualize the NLMs
landscapetools::show_landscape(random_curdling)
landscapetools::show_landscape(wheyed_curdling)

## End(Not run)

nlm_distancegradient

Description

Simulates a distance-gradient neutral landscape model.

Usage

nlm_distancegradient(ncol, nrow, resolution = 1, origin, rescale = TRUE)
nlm_distancegradient(ncol, nrow, resolution = 1, origin, rescale = TRUE)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`origin`	[`numerical(4)`] Edge coordinates of the origin (raster::extent with xmin, xmax, ymin, ymax) of the distance measurement.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1. Otherwise, the distance in raster units is calculated.

Details

The function takes the number of columns and rows as input and creates a RasterLayer with the same extent. Origin is a numeric vector of xmin, xmax, ymin, ymax for a rectangle inside the raster from which the distance is measured.

Value

RasterLayer

Examples


# simulate a distance gradient
distance_gradient <- nlm_distancegradient(ncol = 100, nrow = 100,
                                           origin = c(20, 30, 10, 15))
## Not run: 
# visualize the NLM
landscapetools::show_landscape(distance_gradient)

## End(Not run)
# simulate a distance gradient
distance_gradient <- nlm_distancegradient(ncol = 100, nrow = 100,
                                           origin = c(20, 30, 10, 15))
## Not run: 
# visualize the NLM
landscapetools::show_landscape(distance_gradient)

## End(Not run)

nlm_edgegradient

Description

Simulates an edge-gradient neutral landscape model.

Usage

nlm_edgegradient(ncol, nrow, resolution = 1, direction = NA, rescale = TRUE)
nlm_edgegradient(ncol, nrow, resolution = 1, direction = NA, rescale = TRUE)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`direction`	[`numerical(1)`] Direction of the gradient (between 0 and 360 degrees), if unspecified the direction is randomly determined.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

Simulates a linear gradient orientated on a specified or random direction that has a central peak running perpendicular to the gradient direction.

Value

RasterLayer

References

Travis, J.M.J. & Dytham, C. (2004) A method for simulating patterns of habitat availability at static and dynamic range margins. Oikos, 104, 410–416.

Examples


# simulate random curdling
edge_gradient <- nlm_edgegradient(ncol = 100, nrow = 100, direction = 80)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(edge_gradient)

## End(Not run)

# simulate random curdling
edge_gradient <- nlm_edgegradient(ncol = 100, nrow = 100, direction = 80)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(edge_gradient)

## End(Not run)

nlm_fbm

Description

Creates a two-dimensional fractional Brownian motion neutral landscape model.

Usage

nlm_fbm(
  ncol,
  nrow,
  resolution = 1,
  fract_dim = 1,
  user_seed = NULL,
  rescale = TRUE,
  ...
)
nlm_fbm(
  ncol,
  nrow,
  resolution = 1,
  fract_dim = 1,
  user_seed = NULL,
  rescale = TRUE,
  ...
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`fract_dim`	[`numerical(1)`] The fractal dimension of the process (0,2)
`user_seed`	[`numerical(1)`] Set random seed for the simulation
`rescale`	[`numeric(1)`] If `TRUE` (default), the values are rescaled between 0-1.
`...`	Other options to RandomFields::RFoptions, especially if using a fractal dimension between ~ 1.6 and 1.9 one must set the option `modus_operandi = "sloppy"`.

Details

Neutral landscapes are generated using fractional Brownian motion, an extension of Brownian motion in which the amount of correlation between steps is controlled by frac_dim. A high value of frac_dim produces a relatively smooth, correlated surface while a low value produces a rough, uncorrelated one.

Value

RasterLayer

References

Travis, J.M.J. & Dytham, C. (2004). A method for simulating patterns of habitat availability at static and dynamic range margins. Oikos , 104, 410–416.

Martin Schlather, Alexander Malinowski, Peter J. Menck, Marco Oesting, Kirstin Strokorb (2015). nlm_fBm. Journal of Statistical Software, 63(8), 1-25. URL http://www.jstatsoft.org/v63/i08/.

Examples

# simulate fractional brownian motion
fbm_raster  <- nlm_fbm(ncol = 20, nrow = 30, fract_dim = 0.8)

## Not run: 

# visualize the NLM
landscapetools::show_landscape(fbm_raster)


## End(Not run)

# simulate fractional brownian motion
fbm_raster  <- nlm_fbm(ncol = 20, nrow = 30, fract_dim = 0.8)

## Not run: 

# visualize the NLM
landscapetools::show_landscape(fbm_raster)


## End(Not run)

nlm_gaussianfield

Description

Simulates a spatially correlated random fields (Gaussian random fields) neutral landscape model.

Usage

nlm_gaussianfield(
  ncol,
  nrow,
  resolution = 1,
  autocorr_range = 10,
  mag_var = 5,
  nug = 0.2,
  mean = 0.5,
  user_seed = NULL,
  rescale = TRUE
)
nlm_gaussianfield(
  ncol,
  nrow,
  resolution = 1,
  autocorr_range = 10,
  mag_var = 5,
  nug = 0.2,
  mean = 0.5,
  user_seed = NULL,
  rescale = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`autocorr_range`	[`numerical(1)`] Maximum range (raster units) of spatial autocorrelation.
`mag_var`	[`numerical(1)`] Magnitude of variation over the entire landscape.
`nug`	[`numerical(1)`] Magnitude of variation in the scale of `autocorr_range`, smaller values lead to more homogeneous landscapes.
`mean`	[`numerical(1)`] Mean value over the field.
`user_seed`	[`numerical(1)`] Set random seed for the simulation
`rescale`	[`numeric(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

Gaussian random fields are a collection of random numbers on a spatially discrete set of coordinates (landscape raster). Natural sciences often apply them with spatial autocorrelation, meaning that objects which distant are more distinct from one another than they are to closer objects.

References

Kéry & Royle (2016) Applied Hierarchical Modeling in Ecology Chapter 20

Examples

# simulate random gaussian field
gaussian_field <- nlm_gaussianfield(ncol = 90, nrow = 90,
                                    autocorr_range = 60,
                                    mag_var = 8,
                                    nug = 5)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(gaussian_field)

## End(Not run)

# simulate random gaussian field
gaussian_field <- nlm_gaussianfield(ncol = 90, nrow = 90,
                                    autocorr_range = 60,
                                    mag_var = 8,
                                    nug = 5)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(gaussian_field)

## End(Not run)

nlm_mosaicfield

Description

Simulates a mosaic random field neutral landscape model.

Usage

nlm_mosaicfield(
  ncol,
  nrow,
  resolution = 1,
  n = 20,
  mosaic_mean = 0.5,
  mosaic_sd = 0.5,
  collect = FALSE,
  infinit = FALSE,
  rescale = TRUE
)
nlm_mosaicfield(
  ncol,
  nrow,
  resolution = 1,
  n = 20,
  mosaic_mean = 0.5,
  mosaic_sd = 0.5,
  collect = FALSE,
  infinit = FALSE,
  rescale = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`n`	[`numerical(1)`] Number of steps over which the mosaic random field algorithm is run
`mosaic_mean`	[`numerical(1)`] Mean value of the mosaic displacement distribution
`mosaic_sd`	[`numerical(1)`] Standard deviation of the mosaic displacement distribution
`collect`	[`logical(1)`] return `RasterBrick` of all steps 1:`n`
`infinit`	[`logical(1)`] return raster of the random mosaic field algorithm with infinite steps
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Value

RasterLayer or List with RasterLayer/s and/or RasterBrick

References

Schwab, Dimitri, Martin Schlather, and Jürgen Potthoff. "A general class of mosaic random fields." arXiv preprint arXiv:1709.01441 (2017).
Baddeley, Adrian, Ege Rubak, and Rolf Turner. Spatial point patterns: methodology and applications with R. CRC Press, 2015.

Examples


# simulate mosaic random field
mosaic_field <- nlm_mosaicfield(ncol = 100,
                                nrow = 200,
                                n = NA,
                                infinit = TRUE,
                                collect = FALSE)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaic_field)

## End(Not run)

# simulate mosaic random field
mosaic_field <- nlm_mosaicfield(ncol = 100,
                                nrow = 200,
                                n = NA,
                                infinit = TRUE,
                                collect = FALSE)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaic_field)

## End(Not run)

nlm_mosaicgibbs

Description

Simulate a neutral landscape model using the Gibbs algorithm introduced in Gaucherel (2008).

Usage

nlm_mosaicgibbs(
  ncol,
  nrow,
  resolution = 1,
  germs,
  R,
  patch_classes,
  rescale = TRUE
)
nlm_mosaicgibbs(
  ncol,
  nrow,
  resolution = 1,
  germs,
  R,
  patch_classes,
  rescale = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`germs`	[`numerical(1)`] Intensity parameter (non-negative integer).
`R`	[`numerical(1)`] Interaction radius (non-negative integer) for the fitting of the spatial point pattern process - the min. distance between germs in map units.
`patch_classes`	[`numerical(1)`] Number of classes for germs.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

nlm_mosaicgibbs offers the second option of simulating a neutral landscape model described in Gaucherel (2008). The method works in principal like the tessellation method (nlm_mosaictess), but instead of a random point pattern the algorithm fits a simulated realization of the Strauss process. The Strauss process starts with a given number of points and uses a minimization approach to fit a point pattern with a given interaction parameter (0 - hardcore process; 1 - Poisson process) and interaction radius (distance of points/germs being apart).

Value

RasterLayer

References

Gaucherel, C. (2008) Neutral models for polygonal landscapes with linear networks. Ecological Modelling, 219, 39 - 48.

Examples

# simulate polygonal landscapes
mosaicgibbs <- nlm_mosaicgibbs(ncol = 40,
                              nrow = 30,
                              germs = 20,
                              R = 0.02,
                              patch_classes = 12)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaicgibbs)

## End(Not run)

# simulate polygonal landscapes
mosaicgibbs <- nlm_mosaicgibbs(ncol = 40,
                              nrow = 30,
                              germs = 20,
                              R = 0.02,
                              patch_classes = 12)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaicgibbs)

## End(Not run)

nlm_mosaictess

Description

Simulate a neutral landscape model using the tesselation approach introduced in Gaucherel (2008).

Usage

nlm_mosaictess(ncol, nrow, resolution = 1, germs, rescale = TRUE)
nlm_mosaictess(ncol, nrow, resolution = 1, germs, rescale = TRUE)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`germs`	[`numerical(1)`] Intensity parameter (non-negative integer).
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

nlm_mosaictess offers the first option of simulating a neutral landscape model described in Gaucherel (2008). It generates a random point pattern (germs) with an independent distribution and uses the Voronoi tessellation to simulate mosaic landscapes.

Value

RasterLayer

References

Gaucherel, C. (2008) Neutral models for polygonal landscapes with linear networks. Ecological Modelling, 219, 39 - 48.

Examples

# simulate polygonal landscapes
mosaictess <- nlm_mosaictess(ncol = 30, nrow = 60, germs = 200)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaictess)

## End(Not run)

# simulate polygonal landscapes
mosaictess <- nlm_mosaictess(ncol = 30, nrow = 60, germs = 200)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(mosaictess)

## End(Not run)

nlm_mpd

Description

Simulates a midpoint displacement neutral landscape model.

Usage

nlm_mpd(
  ncol,
  nrow,
  resolution = 1,
  roughness = 0.5,
  rand_dev = 1,
  torus = FALSE,
  rescale = TRUE,
  verbose = TRUE
)
nlm_mpd(
  ncol,
  nrow,
  resolution = 1,
  roughness = 0.5,
  rand_dev = 1,
  torus = FALSE,
  rescale = TRUE,
  verbose = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`roughness`	[`numerical(1)`] Controls the level of spatial autocorrelation (!= Hurst exponent)
`rand_dev`	[`numerical(1)`] Initial standard deviation for the displacement step (default == 1), sets the scale of the overall variance in the resulting landscape.
`torus`	[`logical(1)`] Logical value indicating wether the algorithm should be simulated on a torus (default FALSE)
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.
`verbose`	[`logical(1)`] If `TRUE` (default), the user gets a warning that the functions changes the dimensions to an appropriate one for the algorithm.

Details

The algorithm is a direct implementation of the midpoint displacement algorithm. It performs the following steps:

Initialization: Determine the smallest fit of max(ncol, nrow) in n^2 + 1 and assign value to n. Setup matrix of size (n^2 + 1)*(n^2 + 1). Afterwards, assign a random value to the four corners of the matrix.
Square Step: For each square in the matrix, assign the average of the four corner points plus a random value to the midpoint of that square.
Diamond Step: For each diamond in the matrix, assign the average of the four corner points plus a random value to the midpoint of that diamond.

At each iteration the roughness, an approximation to common Hurst exponent, is reduced.

Value

RasterLayer

References

https://en.wikipedia.org/wiki/Diamond-square_algorithm

Examples


# simulate midpoint displacement
midpoint_displacememt <- nlm_mpd(ncol = 100,
                                 nrow = 100,
                                 roughness = 0.3)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(midpoint_displacememt)

## End(Not run)
# simulate midpoint displacement
midpoint_displacememt <- nlm_mpd(ncol = 100,
                                 nrow = 100,
                                 roughness = 0.3)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(midpoint_displacememt)

## End(Not run)

nlm_neigh

Description

Create a neutral landscape model with categories and clustering based on neighborhood characteristics.

Usage

nlm_neigh(
  ncol,
  nrow,
  resolution = 1,
  p_neigh,
  p_empty,
  categories = 3,
  neighbourhood = 4,
  proportions = NA,
  rescale = TRUE
)
nlm_neigh(
  ncol,
  nrow,
  resolution = 1,
  p_neigh,
  p_empty,
  categories = 3,
  neighbourhood = 4,
  proportions = NA,
  rescale = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`p_neigh`	[`numerical(1)`] Probability of a cell will turning into a value if there is any neighbor with the same or a higher value.
`p_empty`	[`numerical(1)`] Probability a cell receives a value if all neighbors have no value (i.e. zero).
`categories`	[`numerical(1)`] Number of categories used.
`neighbourhood`	[`numerical(1)`] The neighbourhood used to determined adjacent cells: '8 ("Moore")' takes the eight surrounding cells, while '4 ("Von-Neumann")' takes the four adjacent cells (i.e. left, right, upper and lower cells).
`proportions`	[`vector(1)`] The algorithm uses uniform proportions for each category by default. A vector with as many proportions as categories and that sums up to 1 can be used for other distributions.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

The algorithm draws a random cell and turns it into a given category based on the probabilities p_neigh and p_empty, respectively. The decision is based on the probability p_neigh, if there is any cell in the Moore- (8 cells) or Von-Neumann-neighborhood (4 cells), otherwise it is based on p_empty. To create clustered neutral landscape models, p_empty should be (significantly) smaller than p_neigh. By default, the Von-Neumann-neighborhood is used to check adjacent cells. The algorithm starts with the highest categorical value. If the proportion of cells with this value is reached, the categorical value is reduced by 1. By default, a uniform distribution of the categories is applied.

Value

RasterLayer

References

Scherer, Cédric, et al. "Merging trait-based and individual-based modelling: An animal functional type approach to explore the responses of birds to climatic and land use changes in semi-arid African savannas." Ecological Modelling 326 (2016): 75-89.

Examples

# simulate neighborhood model
neigh_raster <- nlm_neigh(ncol = 50, nrow = 50, p_neigh = 0.7, p_empty = 0.1,
                    categories = 5, neighbourhood = 4)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(neigh_raster)

## End(Not run)

# simulate neighborhood model
neigh_raster <- nlm_neigh(ncol = 50, nrow = 50, p_neigh = 0.7, p_empty = 0.1,
                    categories = 5, neighbourhood = 4)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(neigh_raster)

## End(Not run)

nlm_percolation

Description

Generates a random percolation neutral landscape model.

Usage

nlm_percolation(ncol, nrow, resolution = 1, prob = 0.5)
nlm_percolation(ncol, nrow, resolution = 1, prob = 0.5)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`prob`	[`numerical(1)`] Probability value for setting a cell to 1.

Details

The simulation of a random percolation map is accomplished in two steps:

Initialization: Setup matrix of size (ncol*nrow)
Map generation: For each cell in the matrix a single uniformly distributed random number is generated and tested against a probability prob. If the random number is smaller than prob, the cell is set to TRUE - if it is higher the cell is set to FALSE.

Value

RasterLayer

References

1. Gardner RH, O'Neill R V, Turner MG, Dale VH. 1989. Quantifying scale-dependent effects of animal movement with simple percolation models. Landscape Ecology 3:217 - 227.

2. Gustafson, E.J. & Parker, G.R. (1992) Relationships between landcover proportion and indices of landscape spatial pattern. Landscape Ecology , 7, 101 - 110.

Examples

# simulate percolation model
percolation <- nlm_percolation(ncol = 100, nrow = 100, prob = 0.5)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(percolation)

## End(Not run)
# simulate percolation model
percolation <- nlm_percolation(ncol = 100, nrow = 100, prob = 0.5)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(percolation)

## End(Not run)

nlm_planargradient

Description

Simulates a planar gradient neutral landscape model.

Usage

nlm_planargradient(ncol, nrow, resolution = 1, direction = NA, rescale = TRUE)
nlm_planargradient(ncol, nrow, resolution = 1, direction = NA, rescale = TRUE)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`direction`	[`numerical(1)`] Direction of the gradient in degrees, if unspecified the direction is randomly determined.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

Simulates a linear gradient sloping in a specified or random direction.

Value

RasterLayer

References

Palmer, M.W. (1992) The coexistence of species in fractal landscapes. The American Naturalist, 139, 375 - 397.

Examples

# simulate planar gradient
planar_gradient <- nlm_planargradient(ncol = 200, nrow = 200)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(planar_gradient)

## End(Not run)

# simulate planar gradient
planar_gradient <- nlm_planargradient(ncol = 200, nrow = 200)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(planar_gradient)

## End(Not run)

nlm_random

Description

Simulates a spatially random neutral landscape model with values drawn a uniform distribution.

Usage

nlm_random(ncol, nrow, resolution = 1, rescale = TRUE)
nlm_random(ncol, nrow, resolution = 1, rescale = TRUE)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

The function takes the number of columns and rows as input and creates a RasterLayer with the same extent. Each raster cell is randomly assigned a value between 0 and 1 drawn from an uniform distribution (runif(1,0,1)).

Value

RasterLayer

Examples

# simulate spatially random model
random <- nlm_random(ncol = 200, nrow = 100)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(random)

## End(Not run)

# simulate spatially random model
random <- nlm_random(ncol = 200, nrow = 100)

## Not run: 
# visualize the NLM
landscapetools::show_landscape(random)

## End(Not run)

nlm_randomcluster

Description

Simulates a random cluster nearest-neighbour neutral landscape.

Usage

nlm_randomcluster(
  ncol,
  nrow,
  resolution = 1,
  p,
  ai = c(0.5, 0.5),
  neighbourhood = 4,
  rescale = TRUE
)
nlm_randomcluster(
  ncol,
  nrow,
  resolution = 1,
  p,
  ai = c(0.5, 0.5),
  neighbourhood = 4,
  rescale = TRUE
)

Arguments

`ncol`	[`integer(1)`] Number of columns forming the raster.
`nrow`	[`integer(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`p`	[`numerical(1)`] Defines the proportion of elements randomly selected to form clusters.
`ai`	Vector with the cluster type distribution (percentages of occupancy). This directly controls the number of types via the given length.
`neighbourhood`	[`numerical(1)`] Clusters are defined using a set of neighbourhood structures, 4 (Rook's or von Neumann neighbourhood) (default), 8 (Queen's or Moore neighbourhood).
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

This is a direct implementation of steps A - D of the modified random clusters algorithm by Saura & Martínez-Millán (2000), which creates naturalistic patchy patterns.

Value

Raster with random values ranging from 0-1.

References

Saura, S. & Martínez-Millán, J. (2000) Landscape patterns simulation with a modified random clusters method. Landscape Ecology, 15, 661 – 678.

Examples

# simulate random clustering
random_cluster <- nlm_randomcluster(ncol = 30, nrow = 30,
                                     p = 0.4,
                                     ai = c(0.25, 0.25, 0.5))
## Not run: 
# visualize the NLM
landscapetools::show_landscape(random_cluster)

## End(Not run)

# simulate random clustering
random_cluster <- nlm_randomcluster(ncol = 30, nrow = 30,
                                     p = 0.4,
                                     ai = c(0.25, 0.25, 0.5))
## Not run: 
# visualize the NLM
landscapetools::show_landscape(random_cluster)

## End(Not run)

nlm_randomrectangularcluster

Description

Simulates a random rectangular clusters neutral landscape model with values ranging 0-1.

Usage

nlm_randomrectangularcluster(
  ncol,
  nrow,
  resolution = 1,
  minl,
  maxl,
  rescale = TRUE
)
nlm_randomrectangularcluster(
  ncol,
  nrow,
  resolution = 1,
  minl,
  maxl,
  rescale = TRUE
)

Arguments

`ncol`	[`numerical(1)`] Number of columns forming the raster.
`nrow`	[`numerical(1)`] Number of rows forming the raster.
`resolution`	[`numerical(1)`] Resolution of the raster.
`minl`	[`numerical(1)`] The minimum possible width and height for each random rectangular cluster.
`maxl`	[`numerical(1)`] The maximum possible width and height for each random rectangular cluster.
`rescale`	[`logical(1)`] If `TRUE` (default), the values are rescaled between 0-1.

Details

The random rectangular cluster algorithm starts to fill a raster randomly with rectangles defined by minl and maxl until the surface of the landscape is completely covered. This is one type of realisation of a "falling/dead leaves" algorithm, for more details see Galerne & Gousseau (2012).

Value

RasterLayer

References

Gustafson, E.J. & Parker, G.R. (1992). Relationships between landcover proportion and indices of landscape spatial pattern. Landscape ecology, 7, 101–110. Galerne B. & Gousseau Y. (2012). The Transparent Dead Leaves Model. Advances in Applied Probability, Applied Probability Trust, 44, 1–20.

Examples

# simulate random rectangular cluster
randomrectangular_cluster <- nlm_randomrectangularcluster(ncol = 50,
                                                          nrow = 30,
                                                          minl = 5,
                                                          maxl = 10)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(randomrectangular_cluster)

## End(Not run)

# simulate random rectangular cluster
randomrectangular_cluster <- nlm_randomrectangularcluster(ncol = 50,
                                                          nrow = 30,
                                                          minl = 5,
                                                          maxl = 10)
## Not run: 
# visualize the NLM
landscapetools::show_landscape(randomrectangular_cluster)

## End(Not run)

Package 'NLMR'

Help Index

nlm_curds

Description

Usage

Arguments

Details

Value

References

Examples

nlm_distancegradient

Description

Usage

Arguments

Details

Value

See Also

Examples

nlm_edgegradient

Description

Usage

Arguments

Details

Value

References

See Also

Examples

nlm_fbm

Description

Usage

Arguments

Details

Value

References

Examples

nlm_gaussianfield

Description

Usage

Arguments

Details

References

Examples

nlm_mosaicfield

Description

Usage

Arguments

Value

References

Examples

nlm_mosaicgibbs

Description

Usage

Arguments

Details

Value

References

Examples

nlm_mosaictess

Description

Usage

Arguments

Details

Value

References

Examples

nlm_mpd

Description

Usage

Arguments

Details

Value

References

Examples

nlm_neigh

Description

Usage

Arguments

Details

Value

References