MicrobTiSDA

0.1.0

Microbiome Time-Series Data Analysis

0packages depend

2Kdownloads / year

63.8%test coverage

13/13checks pass

Overview

About

Maintained by Shijia LiFirst published 2025-09-221 releasesCRAN page ↗GitHub ↗

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 Details on this package are also described in an unpublished manuscript.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.

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).

Health

CRAN checks

13OK

Slowest check: 16.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.16

63.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,037 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 40%
Documented parameters: 100%
Return-value docs: 100%
References docs: 2%

Downloads

CRAN downloads in the past year

Rank #18,225 · ~6/day · ~169/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

64890 days

2K1 year

Compare downloads with other packages →

Also on90 r2u33 autocran

Repository

GitHub ↗ lishijiagg/microbtisda

5Stars

0Forks

0Open issues

0Open PRs

1Releases

35Commits

2Contributors

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

Stars over time

2025-12-08 · 22026-07-07 · 5

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lishijiagg/microbtisda on 2026-07-19.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

HTML 11,495 (61%)R 4,330 (23%)Rd 2,572 (14%)Vignettes 320 (2%)

Code characteristics

Object systems

S338

Cyclomatic complexity: 3.0 median / 21 max
Test cases: 19 / 0.16 per code line

Test coverage

Line coverage

64%

Expression

54.9%

Tests / Examples

63.8% / 3% ex

Functions

57 19 exported

Complexity

4.1 avg / 21 max

Call network

57 nodes / 1 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

57 functions

Function	Cyclo	Coverage
plot.DataOppCorVis	5	0%
plot.DataRFClassifier	4	0%
plot.MicrobTiSDA.MSERvisual	7	0%
plot.MicrobTiSDA.cluster	4	0%
plot.MicrobTiSDA.clusterCut	4	0%
plot.MicrobTiSDA.visual	7	0%

Datasets

Bundled datasets · 9

Name	Class	Rows × Cols	Also ships in
OSLO.infant.data	data.frame	476,921 × 77	–
OSLO.infant.meta	data.frame	77 × 4	–
OSLO.infant.taxa	data.frame	476,921 × 8	–
fujita.data	data.frame	28 × 880	–
fujita.meta	data.frame	880 × 8	–
fujita.taxa	data.frame	565 × 9	–
preterm.data	data.frame	202 × 51	–
preterm.meta	data.frame	51 × 36	–
preterm.taxa	data.frame	923 × 7	–

People & History

People (1)

Maintainer (1)

Shijia Li

Author, Maintainer

Authors (1)

Shijia Li

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · 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
Installed size: not tracked yet
With dependencies: not tracked yet

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