R Observatory: Metrics for SAFEMCN version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAFEMCN

1.0.0Package record

Network Topology Parameter Analysis with Rarefaction

0packages depend

1.4Kdownloads / year

49.4%test coverage

13/13flavors OK

Overview

About

Maintained by Xiaotong XuCRAN page ↗

Calculate network topology parameters from Operational Taxonomic Unit (OTU) tables with customizable correlation thresholds, parallel processing options, and visualization capabilities including trend fitting, prediction of future sample sizes, and lag-1 autocorrelation (AR1) analysis. Methods are based on co-occurrence network construction via correlation thresholds and graph-theoretic metrics computed with 'igraph'.

Install

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

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

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

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-safemcn

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-SAFEMCN

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-SAFEMCN

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

13OK

CRAN check page ↗

Slowest check: 1.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK7 OK2026-05-29

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

1.4K

CRAN downloads in the past year

Rank #16,425 · ~4/day · ~119/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

76890 days

1.4K1 year

Compare downloads with other packages →

Also on19 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing SAFEMCN adds 53 packages (27 with compiled code, 57 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5.0

Imports (9)

igraph Hmiscparallelggplot2grDevicesgraphicsrlangstatsutils

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Xiaotong Xu

Author, Maintainer since 1.0.0 (2026)

Yue Zheng

Copyright holder

Releases (1)

1.0.0Latest
record
2026-05-28 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-28
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Download size: 9.3 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SAFEMCN")

Format

Xu, X., & Zheng, Y. (2026). SAFEMCN: Network Topology Parameter Analysis with Rarefaction (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SAFEMCN

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 SAFEMCN version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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