R Observatory: Metrics for MicrobTiSDA version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MicrobTiSDA

0.1.0Package record

Microbiome Time-Series Data Analysis

0packages depend

2.5Kdownloads / year

63.8%test coverage

13/13flavors OK

Overview

About

Maintained by Shijia LiCRAN page ↗GitHub ↗Issues ↗

Provides tools specifically designed for analyzing longitudinal microbiome data. This tool integrates seven functional modules, providing a systematic framework for microbiome time-series analysis. For more details on inferences involving interspecies interactions see Fisher (2014) doi:10.1371/journal.pone.0102451. Details on this package are also described in an unpublished manuscript.

Install

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

install.packages("MicrobTiSDA", 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("Lishijiagg/MicrobTiSDA")

Development version from Lishijiagg/MicrobTiSDA. 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-microbtisda

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-MicrobTiSDA

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-MicrobTiSDA

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: 12.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 1,037 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 66
Examples that run: 40%10 run in a plain check · 15 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 84%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (1)

MicrobTiSDA HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #19,103 · ~7/day · ~210/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

69290 days

2.5K1 year

Compare downloads with other packages →

Also on100 r2u3 autocran

How downloads are counted

Repository

lishijiagg/microbtisda ↗Account: Lishijiagg

6Stars

0Forks

0Open issues

0Open PRs

1Releases

35Commits

2Commit identities

License file reads as MIT · 35 commits · Last activity 2025-09-29 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-12-08 · 22026-09-05 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/lishijiagg/microbtisda on 2026-10-22.

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing MicrobTiSDA adds 102 packages (57 with compiled code, 88 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5

Imports (20)

caretclusterdplyr ggdendro ggplot2 ggraphMASSmgcvplyr pracma randomForest reshape2 scalessplinesstatstibble tidygraph tidyr vegan visNetwork

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown 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 (1)

Shijia Li

Author, Maintainer since 0.1.0 (2025)

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-09-22 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-22
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 3.2 MB / 9 files
Download size: 5.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MicrobTiSDA")

Format

Li, S. (2025). MicrobTiSDA: Microbiome Time-Series Data Analysis (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MicrobTiSDA

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 MicrobTiSDA version 0.1.0 [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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