samc: Create an samc object

In samc: Spatial Absorbing Markov Chains

Create an samc object

Description

Create an samc object that contains the absorbing Markov chain data

Usage

samc(data, absorption, fidelity, model, options = NULL)

## S4 method for signature 'SpatRaster,SpatRaster,SpatRaster,list'
samc(data, absorption, fidelity, model, options = NULL)

## S4 method for signature 'RasterLayer,RasterLayer,RasterLayer,list'
samc(data, absorption, fidelity, model, options = NULL)

## S4 method for signature 'SpatRaster,SpatRaster,missing,list'
samc(data, absorption, model, options = NULL)

## S4 method for signature 'RasterLayer,RasterLayer,missing,list'
samc(data, absorption, model, options = NULL)

## S4 method for signature 'matrix,matrix,matrix,list'
samc(data, absorption, fidelity, model, options = NULL)

## S4 method for signature 'matrix,matrix,missing,list'
samc(data, absorption, model, options = NULL)

## S4 method for signature 'dgCMatrix,missing,missing,missing'
samc(data, options = NULL)

## S4 method for signature 'matrix,missing,missing,missing'
samc(data, options = NULL)

Arguments

data	A SpatRaster-class or RasterLayer-class or matrix or Matrix package dgCMatrix sparse matrix.
absorption	A SpatRaster-class or RasterLayer-class or matrix
fidelity	A SpatRaster-class or RasterLayer-class or matrix
model	A list with args for constructing a transition matrix.
options	A list of options that changes how the samc behaves computationally.

Details

This function is used to create a samc-class object. There are multiple options for creating this object.

Option 1: Raster or Matrix Maps

samc(data = matrix, absorption = matrix, fidelity = matrix, model = list())

samc(data = SpatRaster, absorption = SpatRaster, fidelity = SpatRaster, model = list())

samc(data = RasterLayer, absorption = RasterLayer, fidelity = RasterLayer, model = list())

The samc-class object can be created from a combination of resistance (or conductance), absorption, and fidelity data. These different landscape data inputs must be the same type (a matrix, SpatRaster, or RasterLayer), and have identical properties, including dimensions, location of NA cells, and CRS (if using raster inputs).

The data and absorption inputs are always mandatory for this approach. The fidelity input is optional. If the fidelity input is not provided, then it is assumed that there is no site fidelity (i.e., individuals will always move to an adjacent cell each time step).

The model parameter is mandatory. It is used when calculating the values for the transition matrix. model must be constructed as a list with a transition function, the number of directions (4 or 8), and if the transition function is symmetric (TRUE or FALSE; currently not used). Here is the template: list(fun = `function`, dir = `numeric`, sym = `logical`)

When using raster inputs, SpatRaster objects (from the terra package) are recommended over RasterLayer objects (from the raster package). Internally, samc is using SpatRaster objects, which means RasterLayer objects are being converted to SpatRaster objects, which is a source of memory inefficiency.

Option 2: P Matrix

samc(data = matrix)

samc(data = dgCMatrix)

The data parameter can be used alone to create a samc-class object directly from a preconstructed P matrix. This matrix must be either a base R matrix, or a sparse matrix (dgCMatrix format) from the Matrix package. It must meet the following requirements:

• The number of rows must equal the number of columns (a square matrix)

• Total absorption must be a single column on the right-hand side of the matrix

• At the bottom of the matrix, there must be a row filled with 0's except for the last element (bottom-right of the matrix diagonal), which must be set to 1

• Every disconnected region of the matrix must have at least one non-zero absorbing value

• Each row must sum to 1

• All values must be in the range of 0-1

Additionally, the columns and rows of the P matrix may be named (e.g., using dimnames(), rowname(), colnames(), etc). When specifying origin or dest inputs to metrics, these names may be used instead of cell numbers. This has the advantage of making the code for an analysis easier to read and interpret, which may also help to eliminate unintentional mistakes. There are two requirements for naming the rows/cols of a P matrix. First, since the P matrix represents a pairwise matrix, the row and column names must be the same. Second, there must be no duplicate names. The exception to these rules is the very last column and the very last row of the P matrix. Since these are not part of the pairwise transition matrix, they may have whatever names the user prefers.

Additional Information

Depending on the data used to construct the samc-class object, some metrics may cause crashes. This is a result of the underlying P matrix having specific properties that make some equations unsolvable. One known case is a P matrix that represents a disconnected graph, which can lead to the cond_passage() function crashing. In terms of raster/matrix inputs, a disconnected graph occurs when one or more pixels/cells are unreachable from other pixels/cells due to the presence of a full barrier made up of NA values. In a raster, these may be obvious as islands but can be as inconspicuous as a rogue isolated pixel. There may be other currently unknown situations that lead to unsolvable metrics.

Future work is planned towards identifying these issues during the creation of the samc-class object and handling them appropriately to prevent inadvertent crashes.

Version 3 Changes

Support for creating samc-class objects from TransitionLayer objects was removed so that the package is not dependent on gdistance.

Version 2 Changes

Version 1.5.0 officially removed support for the deprecated resistance, tr_fun, directions, p_mat, latlon, and override arguments. Old code will have to be updated to the new samc() function structure in order to work.

Value

A samc-class object

Examples

# "Load" the data. In this case we are using data built into the package.
# In practice, users will likely load raster data using the raster() function
# from the raster package.
res_data <- samc::example_split_corridor$res
abs_data <- samc::example_split_corridor$abs
init_data <- samc::example_split_corridor$init


# Make sure our data meets the basic input requirements of the package using
# the check() function.
check(res_data, abs_data)
check(res_data, init_data)

# Setup the details for a random-walk model
rw_model <- list(fun = function(x) 1/mean(x), # Function for calculating transition probabilities
                 dir = 8, # Directions of the transitions. Either 4 or 8.
                 sym = TRUE) # Is the function symmetric?


# Create a `samc-class` object with the resistance and absorption data using
# the samc() function. We use the recipricol of the arithmetic mean for
# calculating the transition matrix. Note, the input data here are matrices,
# not RasterLayers.
samc_obj <- samc(res_data, abs_data, model = rw_model)


# Convert the initial state data to probabilities
init_prob_data <- init_data / sum(init_data, na.rm = TRUE)


# Calculate short- and long-term metrics using the analytical functions
short_mort <- mortality(samc_obj, init_prob_data, time = 50)
short_dist <- distribution(samc_obj, origin = 3, time = 50)
long_disp <- dispersal(samc_obj, init_prob_data)
visit <- visitation(samc_obj, dest = 4)
surv <- survival(samc_obj)


# Use the map() function to turn vector results into RasterLayer objects.
short_mort_map <- map(samc_obj, short_mort)
short_dist_map <- map(samc_obj, short_dist)
long_disp_map <- map(samc_obj, long_disp)
visit_map <- map(samc_obj, visit)
surv_map <- map(samc_obj, surv)

samc documentation built on May 31, 2023, 5:23 p.m.