SAFEMCN

1.0.0

Network Topology Parameter Analysis with Rarefaction

0packages depend

671downloads / year

49.4%test coverage

12/13checks pass

Overview

About

Maintained by Xiaotong XuFirst published 2026-05-281 releasesCRAN 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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

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

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

Code health

Yes

Tests · ratio 0.22

49.4%

Coverage · measured lines

100%

Documentation · exports

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
OK2026-05-29
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

671

CRAN downloads in the past year

Rank #15,827 · ~2/day · ~56/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

67190 days

6711 year

Compare downloads with other packages →

Also on12 r2u2 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (2)

Maintainer (1)

Xiaotong Xu

Author, Maintainer

Authors (1)

Xiaotong Xu

Author, Maintainer

Yue Zheng

Package Timeline

1 release. R releases are shown for context.

1.0.0Latest
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: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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