R Observatory: Metrics for PNC version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PNC

0.2.0Package record

Evaluating Phylogeny as a Proxy for Ecological Similarity

0packages depend

2.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yan HeCRAN page ↗

Provides a trait-based workflow for evaluating whether phylogenetic relatedness is informative about similarity in measured quantitative traits within focal species pools and across multiple communities. Functions support trait data integration, taxon-specific trait extraction, coverage assessment, optional principal component analysis, and estimation of phylogenetic signal using Pagel's lambda or Blomberg's K. Curated quantitative trait datasets are included for plants, birds, mammals, reptiles, amphibians, and fishes. Paired simulations assess how observed patterns of missing trait data affect Pagel's lambda estimates and significance classifications for individual traits. Methods for quantifying phylogenetic signal are based on Pagel (1999) doi:10.1038/44766, Blomberg et al. (2003) doi:10.1111/j.0014-3820.2003.tb00285.x, and Münkemüller et al. (2012) doi:10.1111/j.2041-210X.2012.00196.x.

Changes in 0.2.0

Redesigned pnc() and compnc() for a simpler and more consistent analysis workflow.
Standardized outputs and updated n_sp to reflect the actual number of species used in each analysis.
Improved pnc_robustness() and compnc_robustness() using paired simulations to evaluate sensitivity to observed missing-data patterns.
Added consistency, signal_bias, signal_sd, and n_successful to robustness outputs.
Revised function documentation and examples.

From NEWS.md in the release

Install

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

install.packages("PNC", 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-pnc

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-PNC

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-PNC

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: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 1,688 wordsVignettesNoNEWSYes · 100% structured · mentions 0.2.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15
Examples that run: 73%11 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 80%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #19,386 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

67690 days

2.1K1 year

Compare downloads with other packages →

Also on108 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing PNC adds 36 packages (21 with compiled code, 32 MB of source tarballs). Heaviest: ncbit 9.4 MB, igraph 4.8 MB, maps 2.2 MB.

Depends (1)

R >= 3.5.0

Imports (5)

ape geiger phytoolsstatsutils

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

Datasets

People & History

People (4)

Yan He

Author, Maintainer since 0.1.0 (2025)

Lingfeng Mao

Author

Yu Xia

Author

Rui Yang

Author

Releases (2)

Pick two releases to compare their code metrics.

0.2.0Latest
record
2026-08-29 · current release · diff ↗ ·
removed 2 exports
simulate_K_trait, simulate_lambda_trait
R
R 4.6.0 released · 2026-04-24
0.1.0
record
2025-11-07
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-07
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.8 MB / 8 files
Download size: 3.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PNC")

Format

He, Y., Mao, L., Xia, Y., & Yang, R. (2026). PNC: Evaluating Phylogeny as a Proxy for Ecological Similarity (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PNC

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 PNC version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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