R Observatory: Metrics for ncmR version 0.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ncmR

0.4.0Package record

Fit Neutral Community Model to Microbiome or Ecological Data

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yuxuan HeCRAN page ↗GitHub ↗

Provides tools for fitting the neutral community model (NCM) to assess the role of stochastic processes in community assembly. The package implements the framework of Sloan et al. (2006) doi:10.1111/j.1462-2920.2005.00956.x, enabling users to evaluate neutral dynamics in ecological and microbial communities.

Changes in 0.4.0

NEW FEATURES

Added pie_plot() to show Above, Below and Neutral taxon proportions, with external labels and native ggplot2 theme support.
Added run_app(ncm = ...) to open existing NCM or NCM_group results directly in Figure studio.
Redesigned the Shiny app with a model workspace, live figure preview, chart-specific theme editing, and font and color controls.
Added figure exports in PDF, SVG, PNG, TIFF and JPEG formats, plus reproducible R recipe downloads.

CHANGES

scatter_plot() now uses base_theme and native ggplot2 theme objects for styling. Standalone font, axis-size and legend-placement arguments have been removed; use theme settings instead.
The combined model in grouped results is now stored under .ncm_total instead of all. This name is reserved and appears as "Total model" in Shiny.

BUG FIXES

Fixed custom start, lower and upper argument forwarding, and improved retries and diagnostics for non-converged fits.
Corrected frequency-interval boundary handling and tolerance for numerical roundoff in pie plots.
Preserved numeric and character group labels without overwriting the combined model.

Show all changes in 0.4.0Hide the rest of the changes in 0.4.0

Fixed missing group labels causing unrelated, explicitly selected groups to fail. Samples with missing labels are excluded from individual group fits and retained in the combined fit.
Improved automatic figure initialization and consistency between manual previews, exported figures and R recipes.

From NEWS.md in the release

Install

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

install.packages("ncmR", 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("h-xuanjiu/ncmR")

Development version from h-xuanjiu/ncmR. 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-ncmr

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-ncmR

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-ncmR

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: 2.1 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK4 OK2026-04-11

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.0

READMEYes · 344 wordsVignettesNoNEWSYes · 100% structured · mentions 0.4.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 75%3 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 61%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #12,416 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

33430 days

89290 days

2.8K1 year

Compare downloads with other packages →

Also on46 r2u2 autocran

How downloads are counted

Repository

h-xuanjiu/ncmr ↗Account: h-xuanjiu

1Stars

1Forks

0Open issues

0Open PRs

4Releases

19Commits

1Commit identities

packagercran

License file reads as GPL-3.0 · 19 commits · Last activity 2026-05-21

Responsiveness

not measured

Forks over time

2026-07-14 · 02026-08-10 · 1

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/h-xuanjiu/ncmr on 2026-10-18.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing ncmR adds 84 packages (44 with compiled code, 72 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5

Imports (13)

bslib colourpicker dplyr DT ggplot2 ggtextgridHmisc minpack.lm shiny shinyjs systemfonts zip

LinkingTo (0)

none

Suggests (0)

none

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 (1)

Yuxuan He

Releases (4)

Pick two releases to compare their code metrics.

0.4.0Latest
record
2026-10-21 · current release · diff ↗ ·
added 1 export
pie_plot
0.3.1
record
2026-05-10 · diff ↗ ·
removed 1 export
ggsave_unicode

added 1 export
run_app
R
R 4.6.0 released · 2026-04-24
0.2.0
record
2026-04-19 · diff ↗ ·
added 2 exports
ggsave_unicode, scatter_plot
0.1.0
record
2026-04-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-10
Total releases: 4 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 11 KB / 1 file
Download size: 70 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ncmR")

Format

He, Y. (2026). ncmR: Fit Neutral Community Model to Microbiome or Ecological Data (Version 0.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.ncmR

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 ncmR version 0.4.0 [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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