R Observatory: Metrics for MigConnectivity version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MigConnectivity

0.5.0Package record

Estimate Migratory Connectivity for Migratory Animals

0packages depend

2.8Kdownloads / year

1.7%test coverage

11/13flavors OK

Overview

About

Maintained by Jeffrey A. HostetlerCRAN page ↗GitHub ↗

Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) doi:10.1111/2041-210X.12916, Cohen et al. (2019) doi:10.1111/ecog.03974, Roberts et al. (2023) doi:10.1002/eap.2788, and Hostetler et al. (2025) doi:10.1111/2041-210X.14467 for details on some of these methods.

Changes in 0.5.0

Added functions calcNMC and estNMC to quantify NMC_XY (network migratory connectivity strength) as well as network migratory diversity and abundance-weighted NMC
Edited print and plot functions to be able to present NMC estimates
Added/updated citations to our new migratory connectivity paper
Updated worked example vignette to work with current version of ebirdst package (thanks, Henry Stevens!)
Anchored links to functions from external packages in help files

From inst/NEWS.md in the release

Install

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

install.packages("MigConnectivity", 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("SMBC-NZP/MigConnectivity")

Development version from SMBC-NZP/MigConnectivity. 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-migconnectivity

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-MigConnectivity

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-MigConnectivity

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2ERROR11OK

Check messages

ERRORpackage dependenciesr-release-macos-arm64, r-release-macos-x86_64

Package required but not available: ‘RMark’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 3.4 min · r-oldrel-windows-x86_64

Status changes

ERROR11 OK, 2 ERRORNow
ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 135 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.5.0Citation fileNo

Help pages: 33
Examples that run: 45%9 run in a plain check · 11 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 79%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 36%

Vignettes (3)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #17,749 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

71990 days

2.8K1 year

Compare downloads with other packages →

Also on80 r2u10 autocran

How downloads are counted

Repository

smbc-nzp/migconnectivity ↗Organization: SMBC-NZP

8Stars

3Forks

3Open issues

1Open PRs

16Releases

556Commits

7Commit identities

556 commits · Last activity 2025-08-01 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 488
Median days to close, 50 most recently updated closed PRs: 172

Stars over time

2024-09-13 · 82026-07-07 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/smbc-nzp/migconnectivity on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2025-08-01

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing MigConnectivity adds 41 packages (26 with compiled code, 46 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, gplots 4.6 MB.

Depends (1)

R >= 3.5.0

Imports (16)

coda geodist gplotsgraphicsgrDevicesMASSmethodsncf R2jags RMark sf shapestatsterrautilsVGAM

LinkingTo (0)

none

Suggests (4)

knitr maps rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Jeffrey A. Hostetler

Maintainer since 0.4.5 (2024), Author

Michael T. Hallworth

Author

Emily B. Cohen

Contributor

Valentine Herrmann

Contributor · added in 0.4.6

Clark S. Rushing

Contributor

Henry Stevens

Contributor · added in 0.5.0

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
2025-08-27 · current release · diff ↗ ·
added 2 exports
calcNMC, estNMC
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.7
record
2024-03-26 · diff ↗
0.4.6
record
2024-03-18 · diff ↗
0.4.5
record
2024-01-16
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-16
Total releases: 4 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.4 MB / 10 files
Download size: 2.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MigConnectivity")

Format

Hostetler, J. A., Cohen, E. B., Hallworth, M. T., Herrmann, V., Rushing, C. S., & Stevens, H. (2025). MigConnectivity: Estimate Migratory Connectivity for Migratory Animals (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MigConnectivity

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for MigConnectivity version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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