R Observatory: Metrics for pctax version 0.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pctax

0.1.7Package record

Professional Comprehensive Omics Data Analysis

0packages depend

15.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Chen PengCRAN page ↗GitHub ↗Issues ↗

Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and professional omics data analysis.

Install

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

install.packages("pctax", 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("Asa12138/pctax")

Development version from Asa12138/pctax. 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-pctax

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-pctax

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-pctax

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: 4.9 min · r-oldrel-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
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.7

READMEYes · 200 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 0.1.7Citation fileYes · cites a publication

Help pages: 90 (3 internal)includes a package overview page
Examples that run: 66%35 run in a plain check (9 of them under a condition) · 10 only when donttest examples are enabled (R CMD check --as-cran) · 8 never run
Exported functions with examples: 68%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 10%

Vignettes (1)

pctax

How these are measured

Downloads

15.4K

CRAN downloads in the past year

Rank #10,234 · ~42/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

38730 days

1K90 days

15.4K1 year

Compare downloads with other packages →

Also on80 r2u5 autocran

How downloads are counted

Repository

asa12138/pctax ↗Account: Asa12138

32Stars

4Forks

0Open issues

1Open PRs

0Releases

69Commits

2Commit identities

microbiomeromics

69 commits · Last activity 2026-04-03 · 0% stars, 30d · Default branch at 0.1.8, ahead of CRAN 0.1.7 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-03 · 232026-08-31 · 32

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/asa12138/pctax on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-03 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

61 external dependencies (excludes base and recommended)

Installing pctax adds 88 packages (43 with compiled code, 81 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

Depends (1)

R >= 4.2.0

Imports (18)

pcutils dplyr readr ggplot2 vegan magrittrgrDevicesRColorBrewer ggrepel reshape2statstibbleutilsggpubr patchwork ggnewscale ade4 scales

LinkingTo (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)

Chen Peng

Author, Maintainer since 0.1.0 (2024)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.7Latest
record
2026-02-09 · current release · diff ↗ ·
added 13 exports
batch_mediate, drop_tips_update, load_mpa_df, multi_conf, plot_checkm2_res, plot_contigs_quality, plot_gtdb_tr, plot_one_phage, pre_assembly_stats, pre_format_report, pre_genomad, pre_gtdb_tk, stamp_plot
R
R 4.5.0 released · 2025-04-11
0.1.3
record
2024-12-02 · diff ↗ ·
added 3 exports
convert_taxon_name, plot_two_tree, tax_lca
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-04-10
0.1.1
record
2024-04-10 · diff ↗ ·
added 1 export
plot_element_cycle
archivedRemoved from CRAN
2024-03-10
requires archived package 'pcutils'
0.1.0
record
2024-02-27
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-27
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 419 KB / 3 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("pctax")

The package provides a citation file, so citation() returns the authors' own entry.

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 pctax version 0.1.7 [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.

Report a problem with this page →