samc class

S4 class to manage SAMC data.

Details

The samc class is used to help ensure that the package is used correctly and to minimize the possibility for users to accidentally produce nonsensical results that may not be obviously incorrect. This class contains the p matrix necessary for all the calculations in the package, and enforces its type so that users are less likely to inadvertently alter it in a way that will cause issues in calculations.

The samc() function is used to create samc-class objects.

The samc-class slots are subject to change, so users should not be using the @ operator to access or change them. Doing so leads to the risk of broken code in the future. Instead, where relevant, the $ operator can be used to get and set components of the class safely. This is a current list of what can be accessed and modified in the class:

• override

  Some analyses are memory intensive and have the potential to make a user's system non-responsive or crash. By default, a samc-class object cannot be used in these analyses to prevent unintentional loss of work. In some cases, users may wish to use these particular analyses, in which case this behavior can be overridden. To get the current state of the override, use samc_obj$override. To enable the use of the analyses, the override can be set to TRUE using samc_obj$override <- TRUE. Before enabling the override, users should familiarize themselves with the Performance vignette.

• q_matrix

  Advanced users may wish to have direct access to the Q matrix for developing custom calculations/analyses. Assumptions should not be made about the internal storage and management of the P and Q matrices in the samc-class; these things are subject to change in the future. To safely access the Q matrix, use samc_obj$q_matrix. The Q matrix inside of the samc-class cannot be modified.

• p_matrix

  samc_obj$p_matrix can be used to get a copy of the P matrix.

• abs_states

  Used to attach additional absorbing states to an samc object. This does not cause P/Q matrices to be updated. Instead, it is intended to provide decomposed results from the mortality() and absorption() metrics for different sources of absorption that might be contributing to the total absorption values that were used to create the samc object.

  The input must be in the same form as the absorption inputs used in samc(). Matrices are passed in as a list, and rasters are passed in as a RasterStack. Using NA as the input will reset it.

• solver

  samc_obj$solver can be used to change the default linear algebra solver used in some of the metrics. The default value of "direct" means a direct solver is used, and is what was used in previous versions of the package. The alternative value of "iter" switches the package to an iterative solver, which is significantly more memory efficient for larger datasets, but in general will be noticeably slower depending on patterns in the data.

• threads

  samc_obj$threads can be used to get or set the number of threads used for parallel computations. Details can be found in the Parallel Computing vignette.

Slots

data

Data associated with different components of the P matrix

conv_cache

Convolution cache

model

List containing model info used to build the samc object

source

Information about the data source for the P matrix

nodes

The number of nodes in the graph

map

Used to verify landscape inputs and mapping of vector data

crw_map

Matrix used to map location and direction to edges description

prob_mat

Matric for CRW probabilities

names

Names of the transient states

clumps

Number of discontinuous regions in data

override

Used to prevent accidental use of memory intensive functions

solver

Controls the linear solver used for relevant metrics

threads

Used for multi-threading

precision

"single" or "double". Only applies to convolution currently.

.cache

Cached data for performance boosts