S4 class to manage SAMC data.
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.
samc() function is used to create
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:
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
To enable the use of the analyses, the override can be set to
samc_obj$override <- TRUE. Before enabling the override, users should
familiarize themselves with the Performance vignette.
Advanced users may wish to have direct access to the Q matrix for developing
custom calculations/analyses. Assumptions should not be made about the internal
storage and management of the P and Q matrices in the samc-class; these things
are subject to change in the future. To safely access the Q matrix, use
samc_obj$q_matrix. The Q matrix inside of the samc-class cannot be
samc_obj$p_matrix can be used to get a copy of the P matrix.
Used to attach additional absorbing states to an samc object. This does not
cause P/Q matrices to be updated. Instead, it is intended to provide decomposed
results from the
absorption() metrics for different sources
of absorption that might be contributing to the total absorption values that
were used to create the samc object.
The input must be in the same form as the absorption inputs used in
Matrices are passed in as a
list, and rasters are passed in as a
NA as the input will reset it.
samc_obj$threads can be used to get or set the number of threads used
for parallel computations. Details can be found in the Parallel Computing
Data associated with different components of the P matrix
Information about the data source for the P matrix
Used to verify landscape inputs and mapping of vector data
Number of discontinuous regions in data
Used to prevent accidental use of memory intensive functions
Used for multi-threading
Cached data for performance boosts