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samc

CRAN_Status_Badge metacran downloads

Introduction

This is an R package that implements functions for working with absorbing Markov chains using theorems described in the book "Finite Markov Chains" by Kemeny and Snell. The design of this package is based on the implementation of these theorems in the framework described by Fletcher et al. (2019), which applies them to spatial ecology. This framework incorporates both resistance and absorption (or mortality) using spatial absorbing Markov chains to provide several short- and long-term predictions for metrics related to connectivity in landscapes. These metrics are listed in Table 1 of Fletcher et al. (2019), as well as the Overview vignette. Despite the ecological context of the package, these functions can be used in any application of absorbing Markov chains.

As of version 3.1.0, this package also supports use of the convolution algorithm described by Hughes et al. (2023). This algorithm uses a moving window approach to calculate many of the same metrics iteratively in a fast and memory efficient manner.

Installation

It is recommended that users install the samc package via CRAN, where it will be regularly kept up to date.

install.packages("samc")

Citation

When using the package, please cite it using:

Marx, A.J., Wang, C., Sefair, J.A., Acevedo, M.A. and Fletcher, R.J., Jr. (2020), samc: an R package for connectivity modeling with spatial absorbing Markov chains. Ecography, 43: 518-527. doi:10.1111/ecog.04891

Publications

This is a list of publications where the samc package was used in some way:

Major Changes

Version 4 of the package made one breaking change:

  • The visitation_net(samc, origin, dest) function has been updated to behave consistently like other metrics. Instead of a returning a vector, it now returns a single value. This is accompanied with a change to the mathematical implementation the correctly generalizes to models with multiple absorbing points.

Version 3 of the package made some minor breaking changes:

  • The samc() function no longer supports TransitionLayer inputs. This only had a niche use case, but before v3 wasn't an issue to include because of other dependencies on gdistance. With v3, this became the only dependency left for gdistance, so it was removed to avoid potential future issues should gdistance ever get removed from CRAN (which nearly happened in 2022).
  • With the addition of terra support, the map() function was updated so that its output matches the input type to samc(). Previously, matrix inputs were matched to RasterLayers, but now they are mapped back to matrices.
  • The sym option for creating the samc object is currently ignored.
  • The tr_args and occ parameters were renamed to model and init, respectively.
  • cond_passage() and visitation() had an init argument inserted to match the usage of other metrics. These arguments are not fully implemented as of v3.0.0 but may be implemented in the future.
  • Cells are no longer automatically named by samc() when creating the transition matrix from maps. Generating unique character names for each cell ended up being a significant waste of memory as the inputs to samc() got larger. It's unlikely these names were ever used in practice, since using the numeric results from locate() is more convenient.

Version 2 of the package officially removed support for various deprecated parameters in the samc() function. Deprecation warnings were provided starting in v1.4.0 of the package, along with message details and a backward compatible implementation of the expected changes. Removing this backward compatibility is a breaking change that will require some old code to be updated in order to run on the latest version of the package. The changes needed are straightforward and mostly entail some reorganization of the input parameters for the samc() function. Some of the old functionality, primarily overriding memory safety limits, has been moved to the samc-class itself and is no longer tied to the object creation. Redesigning the samc() function and removing backward compatibility makes maintaining the package and adding new features later a substantially improved process; hopefully with only minor inconvenience to users.

Support

Please note that this section is for package-specific queries. If you have questions or comments about the related published articles, contact the authors.

Have an error and can't fix it?

If you have an error, make sure you are using the newest version of the package. Then, check the site's Troubleshooting page, which is periodically updated with common errors that users encounter.

Not sure how to do something? Found a bug? Have a feature request? Still can't solve your error? Want to show off your project?

We have a Github discussions page for anything and everything related to the package here: Github Discussions

License

By default, package code is licensed under AGPLv3. Some code files derived from 3rd party sources may be licensed under GPLv3 and will have a comment to indicate this is the case.

Website materials are licensed under CC BY-NC-SA 4.0.

References

Fletcher, R.J., Jr., Sefair, J.A., Wang, C., Poli, C.L., Smith, T.A.H., Bruna, E.M., Holt, R.D., Barfield, M., Marx, A.J. and Acevedo, M.A. (2019), Towards a unified framework for connectivity that disentangles movement and mortality in space and time. Ecol Lett, 22: 1680-1689. https://doi.org/10.1111/ele.13333

Hughes, J., Lucet, V., Barrett, G. et al. Comparison and parallel implementation of alternative moving-window metrics of the connectivity of protected areas across large landscapes. Landsc Ecol (2023). https://doi.org/10.1007/s10980-023-01619-9