R Observatory: Metrics for phymapnet version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phymapnet

0.1.3Package record

Phylogeny-Guided Bayesian Microbial Network Inference

0packages depend

2Kdownloads / year

84.0%test coverage

13/13flavors OK

Overview

About

Maintained by Rosa AghdamCRAN page ↗

Implements a phylogeny-aware Bayesian graphical modeling framework for microbial network inference using a shrinkage precision estimator guided by a phylogenetic kernel, with optional hyperparameter-ensemble edge reliability analysis.

Install

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

install.packages("phymapnet", 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-phymapnet

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-phymapnet

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-phymapnet

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: 48 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMEYes · 80 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6 (3 internal)
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #16,482 · ~6/day · ~170/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

76790 days

2K1 year

Compare downloads with other packages →

Also on50 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing phymapnet adds 9 packages (8 with compiled code, 11 MB of source tarballs). Heaviest: compositions 2.7 MB, robustbase 2.2 MB, bayesm 2.1 MB.

Depends (0)

none

Imports (3)

statsape compositions

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Rosa Aghdam

Author, Maintainer since 0.1.2 (2026)

Releases (2)

Pick two releases to compare their code metrics.

0.1.3Latest
record
2026-05-26 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.2
record
2026-02-25
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-25
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: 7.7 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phymapnet")

Format

Aghdam, R. (2026). phymapnet: Phylogeny-Guided Bayesian Microbial Network Inference (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.phymapnet

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 phymapnet version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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