Background | The samc-class | Option 1: Maps | Option 2: P Matrix | Option 3: igraph | Utility Functions | Analytical Functions | Initial State Data | Built-in Example Data
Package: samc 4.0.0
Andrew Marx
samc: Spatial Absorbing Markov Chains
Implements functions for working with absorbing Markov chains. The implementation is 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. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.
Authors:
samc_4.0.0.tar.gz
samc_4.0.0.zip(r-4.7)samc_4.0.0.zip(r-4.6)samc_4.0.0.zip(r-4.5)
samc_4.0.0.tgz(r-4.6-x86_64)samc_4.0.0.tgz(r-4.6-arm64)samc_4.0.0.tgz(r-4.5-x86_64)samc_4.0.0.tgz(r-4.5-arm64)
samc_4.0.0.tar.gz(r-4.7-arm64)samc_4.0.0.tar.gz(r-4.7-x86_64)samc_4.0.0.tar.gz(r-4.6-arm64)samc_4.0.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
samc/json (API)
| # Install 'samc' in R: |
| install.packages('samc', repos = c('https://andrewmarx.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/andrewmarx/samc/issues
Pkgdown/docs site:https://andrewmarx.github.io
Datasets:
- example_maze - Simple maze example
- example_split_corridor - Simple split corridor example
- example_toy_res - Toy resistance data
absorbing-markov-chainsconnectivitylandscape-ecologylandscape-metricsmarkov-chaincpp
Last updated from:d090370150. Checks:12 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 334 | ||
| linux-devel-x86_64 | OK | 368 | ||
| source / vignettes | OK | 293 | ||
| linux-release-arm64 | OK | 342 | ||
| linux-release-x86_64 | OK | 392 | ||
| macos-release-arm64 | OK | 331 | ||
| macos-release-x86_64 | OK | 433 | ||
| macos-oldrel-arm64 | OK | 313 | ||
| macos-oldrel-x86_64 | OK | 614 | ||
| windows-devel | OK | 341 | ||
| windows-release | OK | 416 | ||
| windows-oldrel | OK | 409 | ||
| wasm-release | FAIL | 128 |
Exports:absorptioncheckcond_passagedispersaldistributionlocatemapmortalitypairwiserasterizesamcsurvivalvisitationvisitation_net
Dependencies:bootcircularlatticeMatrixmvtnormrasterRcppRcppEigenRcppThreadspterra
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate absorption metrics | absorption absorption,samc,ANY,missing-method absorption,samc,missing,location-method absorption,samc,missing,missing-method |
| Check landscape data | check check,matrix,matrix-method check,matrix,missing-method check,Raster,missing-method check,Raster,Raster-method check,samc,matrix-method check,samc,numeric-method check,samc,Raster-method check,samc,SpatRaster-method check,SpatRaster,missing-method check,SpatRaster,SpatRaster-method |
| Conditional Mean First Passage Time | cond_passage cond_passage,samc,ANY,missing,location-method cond_passage,samc,missing,location,location-method cond_passage,samc,missing,missing,location-method |
| Calculate dispersal metrics | dispersal dispersal,samc,ANY,missing,location,missing-method dispersal,samc,ANY,missing,location,numeric-method dispersal,samc,ANY,missing,missing,missing-method dispersal,samc,missing,location,location,missing-method dispersal,samc,missing,location,location,numeric-method dispersal,samc,missing,location,missing,missing-method dispersal,samc,missing,missing,location,missing-method dispersal,samc,missing,missing,location,numeric-method dispersal,samc,missing,missing,missing,missing-method |
| Calculate distribution metrics | distribution distribution,samc,ANY,missing,location,numeric-method distribution,samc,ANY,missing,missing,numeric-method distribution,samc,missing,location,location,numeric-method distribution,samc,missing,location,missing,numeric-method distribution,samc,missing,missing,location,numeric-method distribution,samc,missing,missing,missing,numeric-method |
| Simple maze example | example_maze |
| Simple split corridor example | example_split_corridor |
| Toy resistance data | example_toy_res |
| Get cell numbers | locate locate,samc,ANY-method locate,samc,missing-method |
| location class | location-class |
| Map vector data | map map,samc,list-method map,samc,numeric-method |
| Calculate mortality metrics | mortality mortality,samc,ANY,missing,location,missing-method mortality,samc,ANY,missing,location,numeric-method mortality,samc,ANY,missing,missing,missing-method mortality,samc,ANY,missing,missing,numeric-method mortality,samc,missing,location,location,missing-method mortality,samc,missing,location,location,numeric-method mortality,samc,missing,location,missing,missing-method mortality,samc,missing,location,missing,numeric-method mortality,samc,missing,missing,location,missing-method mortality,samc,missing,missing,location,numeric-method mortality,samc,missing,missing,missing,missing-method mortality,samc,missing,missing,missing,numeric-method |
| Pairwise analyses | pairwise pairwise,function,samc,location,location-method pairwise,function,samc,location,missing-method |
| Rasterize input | rasterize rasterize,matrix-method rasterize,RasterLayer-method rasterize,SpatRaster-method |
| Create an samc object | samc samc,dgCMatrix,missing,missing,missing-method samc,matrix,matrix,matrix,list-method samc,matrix,matrix,missing,list-method samc,matrix,missing,missing,missing-method samc,RasterLayer,RasterLayer,missing,list-method samc,RasterLayer,RasterLayer,RasterLayer,list-method samc,SpatRaster,SpatRaster,missing,list-method samc,SpatRaster,SpatRaster,SpatRaster,list-method |
| samc class | samc-class |
| Calculate survival metrics | survival survival,samc,ANY,missing-method survival,samc,missing,location-method survival,samc,missing,missing-method |
| Calculate visitation metrics | visitation visitation,samc,ANY,missing,location,missing-method visitation,samc,ANY,missing,missing,missing-method visitation,samc,ANY,missing,missing,numeric-method visitation,samc,missing,location,location,missing-method visitation,samc,missing,location,location,numeric-method visitation,samc,missing,location,missing,missing-method visitation,samc,missing,location,missing,numeric-method visitation,samc,missing,missing,location,missing-method visitation,samc,missing,missing,location,numeric-method visitation,samc,missing,missing,missing,missing-method visitation,samc,missing,missing,missing,numeric-method |
| Calculate net visitation | visitation_net visitation_net,samc,ANY,missing,location-method visitation_net,samc,ANY,missing,missing-method visitation_net,samc,missing,location,location-method visitation_net,samc,missing,location,missing-method |