samc

4.2.1

Spatial Absorbing Markov Chains

0packages depend

7.8Kdownloads / year

52.9%test coverage

12/13checks pass

Overview

About

Maintained by Andrew MarxFirst published 2019-08-2118 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("samc", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("andrewmarx/samc")

Development version from andrewmarx/samc. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-samc

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-samc

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-samc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 18.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.23

52.9%

Coverage · measured lines

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

7.8K

CRAN downloads in the past year

Rank #5,113 · ~21/day · ~647/mo

Releases R versions

Daily download trend is not available in this view yet.

42130 days

1.7K90 days

7.8K1 year

Compare downloads with other packages →

Also on411 r2u2 autocran

Repository

GitHub ↗ andrewmarx/samc

15Stars

5Forks

4Open issues

0Open PRs

13Releases

768Commits

1Contributors

absorbing-markov-chainsconnectivitycranlandscape-ecologylandscape-metricsmarkov-chainr

License AGPL-3.0 · 768 commits · Last activity 2026-06-20 · 0% stars, 30d

Stars over time

2025-05-01 · 142026-07-07 · 15

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/andrewmarx/samc on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (4)

methodsMatrixraster terra

LinkingTo (3)

Rcpp RcppEigen RcppThread (>= 2.1.3)

Suggests (5)

knitr rmarkdown testthat gdistance viridisLite

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Andrew Marx

Author, Maintainer, Copyright holder

Authors (1)

Andrew Marx

Author, Maintainer, Copyright holder

Contributors (6)

Miguel Acevedo

Contributor

Robert Fletcher

Contributor

Barrett Griffin

Contributor · added in 3.1.0

Hughes Josie

Contributor · added in 3.1.0

Jorge Sefair

Contributor

Chao Wang

Contributor

Andrew Marx

Author, Maintainer, Copyright holder

Package Timeline

18 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
4.2.1Latest
2026-03-13 · current release · diff ↗
4.1.0
2026-02-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
4.0.0
2024-10-30 · diff ↗
3.3.0
2024-07-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.2.1
2023-05-09 · diff ↗
3.2.0
2023-05-04 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.1.0
2023-04-07 · diff ↗
3.0.2
2023-02-01 · diff ↗
2.0.1
2022-06-11 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.0
2021-10-23 · diff ↗
1.4.1
2021-09-02 · diff ↗

Show 10 earlier events

1.4.0
2021-06-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.3.0
2021-04-01 · diff ↗
1.2.1
2020-11-03 · diff ↗
1.2.0
2020-10-14 · diff ↗
1.1.0
2020-05-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.4
2020-01-08 · diff ↗
1.0.3
2019-08-21
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-21
Total releases: 18 / 7 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Bundled data: 3.1 KB / 3 files
Download size: 569 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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