This is an R package that implements functions for working with spatial absorbing Markov chains based on the framework described in Toward a unified framework for connectivity that disentangles movement and mortality in space and time by Fletcher et al. in Ecology Letters (2019; DOI: 10.1111/ele.13333). This framework incorporates both resistance and absorption (or mortality) 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.
It is recommended that users install the samc package via CRAN, where it will be regularly kept up to date.
install.packages("samc")Specific versions of the package can be installed by using the ref parameter. In the case of Fletcher et al. (2019), version 0.1.0 of the package was used. To run the code example in the SI of that paper, you would need to install that specific version of samc using:
devtools::install_github("andrewmarx/samc", ref = "0.1.0")Version 1.0.0 and newer requires C++ development tools in order to install from source. The steps required to install the appropriate development tools varies by operating system and is beyond the scope of this document. Users will have to locate and follow appropriate external documentation to setup the devtools if they wish to install the newest version of the samc package from source.
If the devtools are installed and setup correctly, then the latest version of the package can be installed directly from github using the following command:
devtools::install_github("andrewmarx/samc")A paper specific to this package is currently in press at Ecography. Citation info will be added here once available.
Please note that this section is for package specific queries. If you have questions or comments about the related published articles, then you need to contact the authors.
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. If you still cannot solve your issue, or have another programming related question, then Stack Overflow is the place to go. Please respect the rules and etiquette expected there. This includes first checking to see if anyone else has asked similar questions about the samc package. If you can't find an answer, then ask a question. Be sure to include the following information: operating system, R version, samc package version. Also make sure you post relevant code, ideally a self-contained reproducible example that others can run.
If you're getting an error or incorrect output, and are sure it is a bug, then report it as an issue in the GitHub repo (after making sure that it hasn't already been posted). Make sure to include all possible relevant info (operating system, R version, samc version) and a fully reproducible example. Likewise, if you have a feature you'd like to see, submit it to the issue tracker. Keep in mind that my time is limited, so while I do have plans to add new features, I also have other obligations.